diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml
index b6b5ef0d2b..a12daf6469 100644
--- a/galaxy/wrapper/alignmentSieve.xml
+++ b/galaxy/wrapper/alignmentSieve.xml
@@ -63,7 +63,7 @@
             --filteredOutReads '$outFileFiltered'
         #end if
 
-        #if str($shift) != "":
+        #if $shift:
             #set shifts = " ".join(["'{}'".format(x) for x in $shift.split(" ")])
             --shift $shifts
         #elif $ATACshift:
@@ -72,7 +72,7 @@
         #if $BED:
             --BED
             -o '$outFile'
-        #elif str($shift) != "" or $ATACshift:
+        #elif $shift or $ATACshift:
             -o foo.bam &&
             samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam &&
             rm foo.bam
@@ -85,7 +85,7 @@
     <inputs>
         <param name="bamfile" format="bam,cram" type="data" label="BAM file"/>
         <param argument="--BED" type="boolean" label="Output in BEDPE format?" help="Instead of producing BAM files, write output in BEDPE format (as defined by MACS2). Note that only reads/fragments passing filtering criterion are written in BEDPE format."/>
-        <param argument="--shift" type="text" label="Amount to shift fragments" value=""
+        <param argument="--shift" type="text" label="Amount to shift fragments" value="" optional="true" size="30"
             help="Shift the left and right end of a fragment. A positive
                   value shift an end to the right (on the + strand) and
                   a negative value shifts a fragment to the left. Either
diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
index 0e012b5747..5b933ed611 100644
--- a/galaxy/wrapper/bamCompare.xml
+++ b/galaxy/wrapper/bamCompare.xml
@@ -30,11 +30,7 @@
 
             --binSize $binSize
 
-            #if $scaling.method == 'SES':
-                --scaleFactorsMethod SES
-                --sampleLength $scaling.sampleLength
-                --numberOfSamples $scaling.numberOfSamples
-            #elif $scaling.method == 'readCount':
+            #if $scaling.method == 'readCount':
                 --scaleFactorsMethod readCount
             #elif $scaling.method == 'own':
                 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
@@ -46,26 +42,26 @@
             #end if
 
             --operation $comparison.type
-            $exactScaling
 
-            #if $comparison.type in ['ratio','log2']:
+            #if $comparison.type in ['ratio','log2','reciprocal_ratio']:
                 --pseudocount $comparison.pseudocount
             #end if
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
                 #if $advancedOpt.smoothLength:
-                    --smoothLength '$advancedOpt.smoothLength'
+                    --smoothLength $advancedOpt.smoothLength
                 #end if
 
                 @ADVANCED_OPTS_READ_PROCESSING@
+                $advancedOpt.no_collapse
                 $advancedOpt.skipNAs
                 $advancedOpt.skipZeroOverZero
 
-                #if str($advancedOpt.ignoreForNormalization).strip() != '':
+                #if $advancedOpt.ignoreForNormalization:
                     --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
                 #end if
 
@@ -84,17 +80,9 @@
             <param name="method" type="select"
                 label="Method to use for scaling the largest sample to the smallest">
                 <option value="readCount" selected="true">read count</option>
-                <option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option>
                 <option value="own">enter own scaling factors</option>
                 <option value="None">Don't scale reads. Samples can instead be normalized using one of the normalization methods</option>
             </param>
-            <when value="SES">
-                <param argument="--sampleLength" type="integer" value="1000" min="10"
-                    label="Length in bases used to sample the genome and compute the size or scaling factors."
-                    help="The default is fine. Only change it if you know what you are doing."/>
-                <param argument="--numberOfSamples" type="integer" value="100000" min="0"
-                    label="Number of samplings taken from the genome to compute the scaling factors"/>
-            </when>
             <when value="readCount"/>
             <when value="own">
                 <expand macro="scaleFactors"/>
@@ -142,34 +130,26 @@
             </when>
         </conditional>
 
-        <expand macro="exactScaling"/>
         <param name="outFileFormat" type="select" label="Coverage file format">
             <option value="bigwig" selected="true">bigwig</option>
             <option value="bedgraph">bedgraph</option>
         </param>
         <expand macro="region_limit_operation"/>
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <expand macro="smoothLength"/>
-                <expand macro="read_processing_options"/>
-
-                <expand macro="skipNAs"/>
-                <expand macro="skipZeroOverZero"/>
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="smoothLength"/>
+            <expand macro="read_processing_options"/>
+            <expand macro="no_collapse"/>
+            <expand macro="skipNAs"/>
+            <expand macro="skipZeroOverZero"/>
 
-                <param argument="--ignoreForNormalization" type="text" value="" size="50"
-                    label="regions that should be excluded for calculating the scaling factor"
-                    help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
-                        For example, if you know of copy number variations between samples then you may want to exclude these.
-                        Another typical example is the difference in chromosome X copies between males and females in many species.
-                        Example inputs are chrX,chrY,chr3 or chr10:12220-128932"/>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+            <param argument="--ignoreForNormalization" type="text" value="" size="50" optional="true"
+                label="regions that should be excluded for calculating the scaling factor"
+                help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
+                    For example, if you know of copy number variations between samples then you may want to exclude these.
+                    Another typical example is the difference in chromosome X copies between males and females in many species.
+                    Example inputs are chrX,chrY,chr3 or chr10:12220-128932"/>
+            <expand macro="blacklist"/>
+        </expand>
     </inputs>
     <outputs>
         <data format="bigwig" name="outFileName">
@@ -183,19 +163,20 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="no"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="5"/>
-            <param name="type" value="ratio"/>
+            <param name="comparison|type" value="ratio"/>
             <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <param name="comparison|type" value="ratio"/>
+            <param name="advancedOpt|no_collapse" value="false"/>
             <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
         </test>
         <!-- Test with BAM and CRAM file as input
@@ -232,11 +213,12 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
-            <param name="pseudocount" value="1 1"/>
+            <param name="advancedOpt|no_collapse" value="false"/>
+            <param name="comparison|type" value="ratio"/>
+            <param name="comparison|pseudocount" value="1 1"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t50\t1"/>
@@ -250,16 +232,16 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
-            <param name="skipZeroOverZero" value="--skipZeroOverZero"/>
+            <param name="comparison|type" value="ratio"/>
+            <param name="advancedOpt|skipZeroOverZero" value="--skipZeroOverZero"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
-                    <has_text_matching expression="3R\t50\t100\t0.67"/>
-                    <has_text_matching expression="3R\t100\t150\t1.33"/>
-                    <has_text_matching expression="3R\t150\t200\t1"/>
+                    <has_text_matching expression="3R\t90\t100\t0.67"/>
+                    <has_text_matching expression="3R\t140\t150\t1.33"/>
+                    <has_text_matching expression="3R\t190\t200\t1"/>
                 </assert_contents>
             </output>
         </test>
@@ -267,11 +249,11 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
-            <param name="skipNAs" value="true"/>
+            <param name="binSize" value="50"/>
+            <param name="comparison|type" value="ratio"/>
+            <param name="advancedOpt|skipNAs" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t100\t150\t1.33"/>
diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml
index 36b6b200cb..963b864b81 100644
--- a/galaxy/wrapper/bamCoverage.xml
+++ b/galaxy/wrapper/bamCoverage.xml
@@ -41,7 +41,6 @@
             #if str($region).strip() != '':
                 --region '$region'
             #end if
-            $exactScaling
 
             #if $advancedOpt.showAdvancedOpt == "yes":
                 #if str($advancedOpt.scaleFactor).strip() != '':
@@ -96,58 +95,50 @@
             <option value="bigwig" selected="true">bigwig</option>
             <option value="bedgraph">bedgraph</option>
         </param>
-        <expand macro="exactScaling"/>
         <expand macro="region_limit_operation"/>
 
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="scaleFactor"/>
+            <expand macro="smoothLength"/>
+
+            <param argument="ignoreForNormalization" type="text" value=""
+                label="Regions that should be excluded for normalization"
+                help="A list of chromosome names separated by spaces
+                    containing those chromosomes that should be excluded
+                    during normalization. This is useful when
+                    considering samples with unequal coverage across
+                    chromosomes, like male and female samples. Example: chrX chrM"/>
+
+            <expand macro="skipNAs"/>
+            <expand macro="read_processing_options"/>
+
+            <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
+                label="Determine nucleosome positions from MNase-seq data"
+                help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options."/>
+
+            <param argument="--Offset" type="text"  value="" optional="true"
+                label="Offset inside each alignment to use for the signal location."
+                help="Uses this offset inside of each read as the signal. This is useful in
+                    cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
+                    should be used to denote where the signal is (rather than the span of the
+                    whole alignment). This can be paired with the --filterRNAstrand option. Note
+                    that negative values indicate offsets from the end of each read. A value of
+                    1 indicates the first base of the alignment (taking alignment orientation
+                    into account). Likewise, a value of -1 is the last base of the alignment. An
+                    offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
+                    used to specify a range of positions. Note that specifying something like
+                    --Offset 5 -1 will result in the 5th through last position being used, which
+                    is equivalent to trimming 4 bases from the 5-prime end of alignments."/>
+
+            <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
+                help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
+                        Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
                 <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
+                <option value="forward">forward</option>
+                <option value="reverse">reverse</option>
             </param>
-            <when value="no"/>
-            <when value="yes">
-                <expand macro="scaleFactor"/>
-                <expand macro="smoothLength"/>
-
-                <param argument="ignoreForNormalization" type="text" value=""
-                    label="Regions that should be excluded for normalization"
-                    help="A list of chromosome names separated by spaces
-                        containing those chromosomes that should be excluded
-                        during normalization. This is useful when
-                        considering samples with unequal coverage across
-                        chromosomes, like male and female samples. Example: chrX chrM"/>
-
-                <expand macro="skipNAs"/>
-                <expand macro="read_processing_options"/>
-
-                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
-                    label="Determine nucleosome positions from MNase-seq data"
-                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options."/>
-
-                <param argument="--Offset" type="text"  value="" optional="True"
-                    label="Offset inside each alignment to use for the signal location."
-                    help="Uses this offset inside of each read as the signal. This is useful in
-                        cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
-                        should be used to denote where the signal is (rather than the span of the
-                        whole alignment). This can be paired with the --filterRNAstrand option. Note
-                        that negative values indicate offsets from the end of each read. A value of
-                        1 indicates the first base of the alignment (taking alignment orientation
-                        into account). Likewise, a value of -1 is the last base of the alignment. An
-                        offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
-                        used to specify a range of positions. Note that specifying something like
-                        --Offset 5 -1 will result in the 5th through last position being used, which
-                        is equivalent to trimming 4 bases from the 5-prime end of alignments."/>
-
-                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
-                    help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
-                          Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
-                    <option value="no" selected="true">no</option>
-                    <option value="forward">forward</option>
-                    <option value="reverse">reverse</option>
-                </param>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+            <expand macro="blacklist"/>
+        </expand>
     </inputs>
     <outputs>
         <data format="bigwig" name="outFileName">
@@ -162,8 +153,8 @@
         <test expect_num_outputs="1">
             <param name="bamInput" value="testA.bam" ftype="bam"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="showAdvancedOpt" value="no"/>
-            <param name="type" value="no"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
+            <param name="scaling|type" value="no"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t100\t0"/>
@@ -174,19 +165,16 @@
             </output>
         </test>
 
-        <!-- Test skipNAs for bamCoverage-->
+<!-- Test skipNAs for bamCoverage-->
         <test expect_num_outputs="1">
             <param name="bamInput" value="testA.bam" ftype="bam"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="showAdvancedOpt" value="no"/>
-            <param name="type" value="no"/>
-            <param name="skipNAs" value="true"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|skipNAs" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
-                    <has_text_matching expression="3R\t0\t100\t0"/>
-                    <has_text_matching expression="3R\t100\t200\t1"/>
-                    <has_text_matching expression="chr_cigar\t0\t50\t1"/>
-                    <has_text_matching expression="chr_cigar\t50\t200\t0"/>
+                    <has_text_matching expression="3R\t100\t200\t17903410"/>
+                    <has_text_matching expression="chr_cigar\t0\t50\t17903410"/>
                 </assert_contents>
             </output>
         </test>
@@ -194,78 +182,78 @@
         <test expect_num_outputs="1">
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="showAdvancedOpt" value="no"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="no"/>
+            <param name="scaling|type" value="no"/>
             <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="showAdvancedOpt" value="no"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="2451960000"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="2451960000"/>
             <param name="binSize" value="10"/>
             <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="showAdvancedOpt" value="no"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="2451960000"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="2451960000"/>
             <param name="binSize" value="10"/>
             <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph"/>
         </test>
         <test>
             <param name="bamInput" value="phiX.bam" ftype="bam"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="showAdvancedOpt" value="no"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="2451960000"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="2451960000"/>
             <param name="binSize" value="10"/>
             <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig"/>
         </test>
         <test>
             <param name="bamInput" value="phiX.bam" ftype="bam"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="2451960000"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="2451960000"/>
             <param name="binSize" value="10"/>
             <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph"/>
         </test>
         <test>
             <param name="bamInput" value="phiX.bam" ftype="bam"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="filterRNAstrand" value="reverse"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="2451960000"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|filterRNAstrand" value="reverse"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="2451960000"/>
             <param name="binSize" value="10"/>
             <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig"/>
         </test>
         <test>
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="binSize" value="10"/>
-            <param name="Offset" value="-4 -1"/>
-            <param name="doExtend" value="yes"/>
-            <param name="minMappingQuality" value="0"/>
-            <param name="type" value="no"/>
+            <param name="advancedOpt|Offset" value="-4 -1"/>
+            <param name="advancedOpt|doExtendCustom|doExtend" value="yes"/>
+            <param name="advancedOpt|minMappingQuality" value="0"/>
+            <param name="scaling|type" value="no"/>
             <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig"/>
         </test>
 
         <!-- Test bamCoverage with filter blacklist-->
         <test expect_num_outputs="1">
             <param name="bamInput" value="coverage_filtering.bam" ftype="bam"/>
-            <param name="blackListFileName" value="coverage_filtering.blacklist.bed"/>
+            <param name="advancedOpt|blackListFileName" value="coverage_filtering.blacklist.bed"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="type" value="1x"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="1400"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="scaling|type" value="1x"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="scaling|effectiveGenomeSize|effectiveGenomeSize" value="1400"/>
             <output name="outFileName" file="coverage_filtered.bg" ftype="bedgraph"></output>
         </test>
     </tests>
diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml
index a7eb0d96e4..d6a8222aeb 100644
--- a/galaxy/wrapper/bamPEFragmentSize.xml
+++ b/galaxy/wrapper/bamPEFragmentSize.xml
@@ -11,28 +11,25 @@
         @BINARY@
             @THREADS@
             --bamfiles #echo " ".join($files)
-            #if $samplesLabel:
-                --samplesLabel #echo " ".join($samplesLabel)
-            #else:
-                --samplesLabel #echo " ".join($labels)
-            #end if
+            --samplesLabel #echo ' '.join($labels)#           
             #if $histogram:
                 --histogram '$histogram_outfile'
                 --plotFileFormat '$outFileFormat'
             #end if
             --plotTitle '$plotTitle'
             #if $advancedOpt.showAdvancedOpt == 'yes'
-                --binSize '$advancedOpt.binSize'
-                --distanceBetweenBins '$advancedOpt.distanceBetweenBins'
+                --binSize $advancedOpt.binSize
+                --distanceBetweenBins $advancedOpt.distanceBetweenBins
                 $advancedOpt.logScale
-                --maxFragmentLength '$advancedOpt.maxFragmentLength'
-                @blacklist@
+                --maxFragmentLength $advancedOpt.maxFragmentLength
                 #if $advancedOpt.table
                     --table '$table'
                 #end if
                 #if $advancedOpt.outRawFragmentLengths
                     --outRawFragmentLengths '$fragLengths'
                 #end if
+                @blacklist@
+                $advancedOpt.ggplot
             #end if
             > '$outfile'
 ]]>
@@ -43,43 +40,26 @@
         <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
             label="Get the distribution of read/fragment lengths as a histogram"/>
         <expand macro="input_image_file_format"/>
-        <param argument="--samplesLabel" type="text" size="30"
-            label="Labels for the samples (each BAM file) plotted"
-            help="The default is to use the file name of the sample. The sample labels should be separated by
-            spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
-            <sanitizer>
-               <valid initial="string.printable">
-               </valid>
-            </sanitizer>
-        </param>
         <expand macro="plotTitle"/>
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options">
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param argument="--binSize" type="integer" value="1000" min="1" optional="true"
-                    label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
-                <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true"
-                    label="bin spacing, in bases"
-                    help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/>
-                <param argument="--table" type="boolean" truevalue="--table" falsevalue=""
-                    label="Write metrics to a tab-separated file?"
-                    help="Write the read/fragment metrics to a tab-separated file, which is primarily useful for more automated downstream processing."/>
-                <param argument="--outRawFragmentLengths" type="boolean" truevalue="--outRawFragmentLengths" falsevalue=""
-                    label="Write a file containing the read/fragment length information?"
-                    help="Write the read/fragment length distribution underlying the (optional) plot to a file. This can then be processed in R or other downstream applications."/>
-                <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
-                    label="Plot log frequencies"
-                    help="Plot the frequencies on the log10 scale"/>
-                <param argument="--maxFragmentLength" type="integer" min="0" value="0"
-                    label="Maximum fragment length"
-                    help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length"/>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <param argument="--binSize" type="integer" value="1000" min="1"
+                label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
+            <expand macro="distanceBetweenBins" DISTANCE="1000000"/>
+            <param argument="--table" type="boolean" truevalue="--table" falsevalue=""
+                label="Write metrics to a tab-separated file?"
+                help="Write the read/fragment metrics to a tab-separated file, which is primarily useful for more automated downstream processing."/>
+            <param argument="--outRawFragmentLengths" type="boolean" truevalue="--outRawFragmentLengths" falsevalue=""
+                label="Write a file containing the read/fragment length information?"
+                help="Write the read/fragment length distribution underlying the (optional) plot to a file. This can then be processed in R or other downstream applications."/>
+            <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
+                label="Plot log frequencies"
+                help="Plot the frequencies on the log10 scale"/>
+            <param argument="--maxFragmentLength" type="integer" min="0" value="0"
+                label="Maximum fragment length"
+                help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length"/>
+            <expand macro="blacklist"/>
+            <expand macro="ggplot" />
+        </expand>
 
     </inputs>
     <outputs>
@@ -90,7 +70,6 @@
                 <when input="outFileFormat" value="pdf" format="pdf"/>
                 <when input="outFileFormat" value="svg" format="svg"/>
                 <when input="outFileFormat" value="eps" format="eps"/>
-                <when input="outFileFormat" value="plotly" format="html"/>
             </change_format>
         </data>
         <data name="table" format="tabular" label="${tool.name} on ${on_string}: Read/Fragment metrics in tabular format">
@@ -102,17 +81,19 @@
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam"/>
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="histogram" value="True"/>
             <param name="plotTitle" value="Test Plot"/>
             <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt"/>
-            <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size"/>
+            <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="image_diff" eps="0.1"/>
         </test>
         <test expect_num_outputs="3">
-            <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="table" value="True"/>
-            <param name="outRawFragmentLengths" value="yes"/>
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam" ftype="bam"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|table" value="True"/>
+            <param name="advancedOpt|outRawFragmentLengths" value="yes"/>
             <output name="table" file="bamPEFragmentSize_table1.txt" ftype="tabular"/>
             <output name="fragLengths" file="bamPEFragmentSize_lengths1.txt" ftype="tabular"/>
         </test>
diff --git a/galaxy/wrapper/bigwigAverage.xml b/galaxy/wrapper/bigwigAverage.xml
index 79e613d5c4..c338ea7885 100644
--- a/galaxy/wrapper/bigwigAverage.xml
+++ b/galaxy/wrapper/bigwigAverage.xml
@@ -16,18 +16,15 @@
             --outFileName '$outFileName'
             --outFileFormat '$outFileFormat'
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-
               $advancedOpt.skipNAs
               --scaleFactors '$advancedOpt.scaleFactors'
               --binSize $advancedOpt.binSize
-
                 @blacklist@
-
             #end if
 ]]>
     </command>
@@ -38,22 +35,15 @@
             <option value="bedgraph">bedgraph</option>
         </param>
         <expand macro="region_limit_operation"/>
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options">
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param argument="--binSize" type="integer" value="50" min="1"
-                    label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
-                    help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
+        <expand macro="advancedOpt_scaffold">
+            <param argument="--binSize" type="integer" value="50" min="1"
+                label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
+                help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
 
-                <expand macro="skipNAs"/>
-                <param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')"/>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+            <expand macro="skipNAs"/>
+            <param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')"/>
+            <expand macro="blacklist"/>
+        </expand>
     </inputs>
     <outputs>
         <data format="bigwig" name="outFileName">
@@ -66,33 +56,33 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="bigwigs" value="test.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="binSize" value="5"/>
+            <param name="advancedOpt|binSize" value="5"/>
             <output name="outFileName" file="test_compated.bw" ftype="bigwig" compare="sim_size" delta="500"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bigwigs" value="test.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="binSize" value="5"/>
-            <param name="scaleFactors" value="0.5"/>
+            <param name="advancedOpt|binSize" value="5"/>
+            <param name="advancedOpt|scaleFactors" value="0.5"/>
             <output name="outFileName" file="test_half.bw" ftype="bigwig" compare="sim_size" delta="500"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="binSize" value="5"/>
-            <param name="scaleFactors" value="0.5"/>
+            <param name="advancedOpt|binSize" value="5"/>
+            <param name="advancedOpt|scaleFactors" value="0.5"/>
             <output name="outFileName" file="bigwigAverage2.bw" ftype="bigwig" compare="sim_size" delta="500"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="binSize" value="5"/>
-            <param name="scaleFactors" value="1:2"/>
+            <param name="advancedOpt|binSize" value="5"/>
+            <param name="advancedOpt|scaleFactors" value="1:2"/>
             <output name="outFileName" file="test_compated.bw" ftype="bigwig" compare="sim_size" delta="500"/>
         </test>
     </tests>
diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml
index 1752842362..72670c70f5 100644
--- a/galaxy/wrapper/bigwigCompare.xml
+++ b/galaxy/wrapper/bigwigCompare.xml
@@ -21,22 +21,17 @@
                 --pseudocount $comparison.pseudocount
             #end if
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-
               $advancedOpt.skipNAs
+              $advancedOpt.fixedStep
               $advancedOpt.skipZeroOverZero
               --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
               --binSize $advancedOpt.binSize
-
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
-                    --plotTitle '$advancedOpt.plotTitle'
-                #end if
-                @blacklist@
-
+              @blacklist@
             #end if
 ]]>
     </command>
@@ -84,24 +79,17 @@
 
         <expand macro="region_limit_operation"/>
 
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param argument="--binSize" type="integer" value="50" min="1"
-                    label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
-                    help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
-
-                <expand macro="skipNAs"/>
-                <expand macro="skipZeroOverZero"/>
-                <expand macro="scaleFactors"/>
-                <expand macro="plotTitle"/>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <param argument="--binSize" type="integer" value="50" min="1"
+                label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
+                help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
+            <expand macro="skipNAs"/>
+            <expand macro="skipZeroOverZero"/>
+                <param argument="--fixedStep" type="boolean" truevalue="--fixedStep" falsevalue=""
+                    label ="Write out all bins instead of merging neighbouring bins with equal values"/>
+            <expand macro="scaleFactors"/>
+            <expand macro="blacklist"/>
+        </expand>
     </inputs>
     <outputs>
         <data format="bigwig" name="outFileName">
@@ -115,21 +103,31 @@
         <test expect_num_outputs="1">
             <param name="bigwigFile1" value="test.bw" ftype="bigwig"/>
             <param name="bigwigFile2" value="test.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="no"/>
+            <param name="advancedOpt|showAdvancedOpt" value="no"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="binSize" value="5"/>
-            <param name="comparison_select" value="ratio"/>
+            <param name="comparison|comparison_select" value="ratio"/>
             <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bigwigFile1" value="test.bw" ftype="bigwig"/>
             <param name="bigwigFile2" value="test.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="no"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="comparison_select" value="ratio"/>
+            <param name="advancedOpt|binSize" value="10"/>
+            <param name="comparison|comparison_select" value="ratio"/>
             <output name="outFileName" file="bigwigCompare_result2.bg" sort="true" ftype="bedgraph"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig"/>
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="advancedOpt|fixedStep" value="true" />
+            <param name="advancedOpt|binSize" value="10"/>
+            <param name="comparison|comparison_select" value="ratio"/>
+            <output name="outFileName" file="bigwigCompare_result3.bg" sort="true" ftype="bedgraph"/>
+        </test>
+        
     </tests>
     <help>
 <![CDATA[
diff --git a/galaxy/wrapper/computeGCBias.xml b/galaxy/wrapper/computeGCBias.xml
index e04ca2bbff..79f087419e 100644
--- a/galaxy/wrapper/computeGCBias.xml
+++ b/galaxy/wrapper/computeGCBias.xml
@@ -17,7 +17,7 @@
         @BINARY@
             @THREADS@
             --bamfile local_bamInput.bam
-            --GCbiasFrequenciesFile $outFileName
+            --GCbiasFrequenciesFile '$outFileName'
 
             #if $fragmentLength != "":
                 --fragmentLength $fragmentLength
@@ -31,23 +31,23 @@
                 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
             #end if
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-                --sampleSize '$advancedOpt.sampleSize'
-                --regionSize '$advancedOpt.regionSize'
+                --sampleSize $advancedOpt.sampleSize
+                --regionSize $advancedOpt.regionSize
 
                 #if $advancedOpt.extraSampling:
-                    --extraSampling $advancedOpt.extraSampling
+                    --extraSampling '$advancedOpt.extraSampling'
                 #end if
 
                 @blacklist@
             #end if
 
-            #if str($image_format) != 'none':
-                --biasPlot $outImageName
+            #if $image_format != 'none':
+                --biasPlot '$outImageName'
                 --plotFileFormat $image_format
             #end if
 ]]>
@@ -60,28 +60,21 @@
         <expand macro="effectiveGenomeSize"/>
         <expand macro="fragmentLength"/>
         <expand macro="region_limit_operation"/>
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param name="sampleSize" type="integer" value="50000000" min="1"
-                    label="Number of sampling points to consider" help="(--sampleSize)"/>
-                <param name="regionSize" type="integer" value="300" min="1"
-                    label="Region size"
-                    help ="To plot the reads per GC over a region, the size of the region is
-                    required (see below for more details about the method). By default, the bin size
-                    is set to 300 bases, which is close to the standard fragment size of many sequencing
-                    applications. However, if the depth of sequencing is low, a larger bin size will
-                    be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
-                <param name="extraSampling" type="data" format="bed" optional="true"
-                    label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
-                    help="(--extraSampling)"/>
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <param name="sampleSize" type="integer" value="50000000" min="1"
+                label="Number of sampling points to consider" help="(--sampleSize)"/>
+            <param name="regionSize" type="integer" value="300" min="1"
+                label="Region size"
+                help ="To plot the reads per GC over a region, the size of the region is
+                required (see below for more details about the method). By default, the bin size
+                is set to 300 bases, which is close to the standard fragment size of many sequencing
+                applications. However, if the depth of sequencing is low, a larger bin size will
+                be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
+            <param name="extraSampling" type="data" format="bed" optional="true"
+                label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
+                help="(--extraSampling)"/>
+            <expand macro="blacklist"/>
+        </expand>
         <param name="image_format" type="select"
             label="GC bias plot"
             help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)">
@@ -90,7 +83,6 @@
             <option value="pdf">Image in pdf format</option>
             <option value="svg">Image in svg format</option>
             <option value="eps">Image in eps format</option>
-            <option value="plotly">HTML page rendered with plotly</option>
         </param>
     </inputs>
     <outputs>
@@ -105,7 +97,6 @@
                 <when input="image_format" value="pdf" format="pdf"/>
                 <when input="image_format" value="svg" format="svg"/>
                 <when input="image_format" value="eps" format="eps"/>
-                <when input="image_format" value="plotly" format="html"/>
             </change_format>
         </data>
     </outputs>
@@ -113,13 +104,13 @@
         <test expect_num_outputs="1">
             <param name="bamInput" value="paired_chr2L.bam" ftype="bam"/>
             <param name="image_format" value="png"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="regionSize" value="1"/>
-            <param name="ref_source" value="history"/>
-            <param name="input1" value="sequence.2bit"/>
-            <param name="sampleSize" value="10"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="10050"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="advancedOpt|regionSize" value="1"/>
+            <param name="source|ref_source" value="history"/>
+            <param name="source|input1" value="sequence.2bit"/>
+            <param name="advancedOpt|sampleSize" value="10"/>
+            <param name="effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="effectiveGenomeSize|effectiveGenomeSize" value="10050"/>
             <param name="region" value="chr2L"/>
             <param name="image_format" value="none"/>
             <param name="fragmentLength" value="300"/>
diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml
index b2f46cf742..8673050804 100644
--- a/galaxy/wrapper/computeMatrix.xml
+++ b/galaxy/wrapper/computeMatrix.xml
@@ -53,24 +53,26 @@
                     --unscaled3prime $mode.regionStartLength.unscaled3prime
 
                 #end if
-
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
                 --sortRegions '$advancedOpt.sortRegions'
                 --sortUsing '$advancedOpt.sortUsing'
+                #if str($advancedOpt.sortUsingSamples).strip() != "":
+                    --sortUsingSamples '$advancedOpt.sortUsingSamples'
+                #end if                
                 --averageTypeBins '$advancedOpt.averageTypeBins'
                 $advancedOpt.skipZeros
                 $advancedOpt.missingDataAsZero
                 --binSize $advancedOpt.binSize
 
-                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
+                #if $advancedOpt.minThreshold:
                     --minThreshold $advancedOpt.minThreshold
                 #end if
-                #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
+                #if $advancedOpt.maxThreshold:
                     --maxThreshold $advancedOpt.maxThreshold
                 #end if
-                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
+                #if $advancedOpt.scale:
                     --scale $advancedOpt.scale
                 #end if
 
@@ -105,7 +107,7 @@
             </param>
 
             <when value="scale-regions" >
-                <param argument="--regionBodyLength" type="integer" value="500"
+                <param argument="--regionBodyLength" type="integer" value="1000"
                     label="Distance in bases to which all regions are going to be fit" help=""/>
                 <conditional name="regionStartLength">
                     <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
@@ -114,11 +116,11 @@
                     </param>
                     <when value="no"/>
                     <when value="yes">
-                        <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
+                        <param argument="--beforeRegionStartLength" type="integer" value="0" min="1"
                             label="Distance upstream of the region start position"
                             help="If the regions are genes, this would be the
                             distance upstream of the transcription start site."/>
-                        <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
+                        <param argument="--afterRegionStartLength" type="integer" value="0" min="1"
                             label="Distance downstream of the region end position"
                             help="If the regions are genes, this would be the
                             distance downstream of the transcription end site."/>
@@ -143,10 +145,10 @@
                     label="Discard any values after the region end"
                     help="This is useful to visualize the region end when not using the
                     scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/>
-                <param name="beforeRegionStartLength" type="integer" value="1000" min="1"
+                <param name="beforeRegionStartLength" type="integer" value="500" min="1"
                     label="Distance upstream of the start site of the regions defined in the region file"
                     help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
-                <param name="afterRegionStartLength" type="integer" value="1000" min="1"
+                <param name="afterRegionStartLength" type="integer" value="1500" min="1"
                     label="Distance downstream of the end site of the given regions"
                     help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/>
             </when>
@@ -156,62 +158,56 @@
             <expand macro="input_save_matrix_values"/>
         </expand>
 
-        <conditional name="advancedOpt" >
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
+        <expand macro="advancedOpt_scaffold">
+            <param name="binSize" type="integer" value="10" min="1"
+                label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
+                help="(--binSize)"/>
+
+            <expand macro="sortRegionsComputeMatrix"/>
+            <expand macro="sortUsing"/>
+            <expand macro="sortUsingSamples" />
+
+            <param name="averageTypeBins" type="select"
+                label="Define the type of statistic that should be displayed."
+                help="The value is computed for each bin. (--averageTypeBins)">
+                <option value="mean" selected="true">mean</option>
+                <option value="median">median</option>
+                <option value="min">min</option>
+                <option value="max">max</option>
+                <option value="sum">sum</option>
+                <option value="std">std</option>
             </param>
-            <when value="no"/>
-            <when value="yes">
-                <param name="binSize" type="integer" value="50" min="1"
-                    label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
-                    help="(--binSize)"/>
-
-                <expand macro="sortRegionsComputeMatrix"/>
-                <expand macro="sortUsing"/>
-
-                <param name="averageTypeBins" type="select"
-                    label="Define the type of statistic that should be displayed."
-                    help="The value is computed for each bin. (--averageTypeBins)">
-                    <option value="mean" selected="true">mean</option>
-                    <option value="median">median</option>
-                    <option value="min">min</option>
-                    <option value="max">max</option>
-                    <option value="sum">sum</option>
-                    <option value="std">std</option>
-                </param>
 
-                <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
-                    label="Convert missing values to 0?"
-                    help="If set to 'yes', missing values (NAs) are converted
-                     to 0. If you want to use clustering with plotHeatmap
-                     or plotProfile, set this to 'yes'.
-                          The default is to ignore missing values, which will be
-                          depicted as black areas once a heatmap is created.
-                           (--missingDataAsZero)"/>
-
-                <expand macro="skipZeros"/>
-
-                <param name="minThreshold" type="float" optional="True"
-                    label="Minimum threshold"
-                    help="Any region containing a value that is equal or less than this numeric
-                    value will be skipped. This is useful to skip, for example, genes where the
-                    read count is zero for any of the bins which could be the result of
-                    unmappable areas and can bias the overall results. (--minThreshold)"/>
-                <param name="maxThreshold" type="float" optional="True"
-                    label="Maximum threshold"
-                    help="Any region containing a value that is equal or higher that this
-                    numeric value will be skipped. The max threshold is useful to skip those
-                    few regions with very high read counts (e.g. major satellites) that may
-                    bias the average values. (--maxThreshold)"/>
-                <param name="scale" type="float" optional="True" label="Scaling factor"
-                    help="If set, all values are multiplied by this number. (--scale)"/>
-
-                <expand macro="gtf_options"/>
-
-                <expand macro="blacklist"/>
-            </when>
-        </conditional>
+            <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
+                label="Convert missing values to 0?"
+                help="If set to 'yes', missing values (NAs) are converted
+                    to 0. If you want to use clustering with plotHeatmap
+                    or plotProfile, set this to 'yes'.
+                        The default is to ignore missing values, which will be
+                        depicted as black areas once a heatmap is created.
+                        (--missingDataAsZero)"/>
+
+            <expand macro="skipZeros"/>
+
+            <param name="minThreshold" type="float" optional="true"
+                label="Minimum threshold"
+                help="Any region containing a value that is equal or less than this numeric
+                value will be skipped. This is useful to skip, for example, genes where the
+                read count is zero for any of the bins which could be the result of
+                unmappable areas and can bias the overall results. (--minThreshold)"/>
+            <param name="maxThreshold" type="float" optional="true"
+                label="Maximum threshold"
+                help="Any region containing a value that is equal or higher that this
+                numeric value will be skipped. The max threshold is useful to skip those
+                few regions with very high read counts (e.g. major satellites) that may
+                bias the average values. (--maxThreshold)"/>
+            <param name="scale" type="float" optional="true" label="Scaling factor"
+                help="If set, all values are multiplied by this number. (--scale)"/>
+
+            <expand macro="gtf_options"/>
+
+            <expand macro="blacklist"/>
+        </expand>
     </inputs>
     <outputs>
         <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix"/>
@@ -220,32 +216,35 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="regionsFile" value="computeMatrix1.bed" ftype="bed"/>
-            <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="mode_select" value="reference-point"/>
-            <param name="binSize" value="10"/>
-            <param name="sortUsing" value="sum"/>
-            <param name="averageTypeBins" value="sum"/>
-            <param name="beforeRegionStartLength" value="10"/>
-            <param name="afterRegionStartLength" value="10"/>
+            <param name="regionsFiles_0|regionsFile" value="computeMatrix1.bed" ftype="bed"/>
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="mode|mode_select" value="reference-point"/>
+            <param name="advancedOpt|binSize" value="10"/>
+            <param name="advancedOpt|sortUsing" value="sum"/>
+            <param name="advancedOpt|averageTypeBins" value="sum"/>
+            <param name="mode|beforeRegionStartLength" value="10"/>
+            <param name="mode|afterRegionStartLength" value="10"/>
             <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed"/>
-            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="mode_select" value="reference-point"/>
-            <param name="binSize" value="10"/>
-            <param name="beforeRegionStartLength" value="10"/>
-            <param name="afterRegionStartLength" value="10"/>
+            <param name="regionsFiles_0|regionsFile" value="computeMatrix2.bed" ftype="bed"/>
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="computeMatrix2.bw" ftype="bigwig"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="mode|mode_select" value="reference-point"/>
+            <param name="advancedOpt|binSize" value="10"/>
+            <param name="mode|beforeRegionStartLength" value="10"/>
+            <param name="mode|afterRegionStartLength" value="10"/>
             <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed"/>
-            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig"/>
-            <param name="showAdvancedOpt" value="yes"/>
-            <param name="mode_select" value="scale-regions"/>
+            <param name="regionsFiles_0|regionsFile" value="computeMatrix2.bed" ftype="bed"/>
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="computeMatrix2.bw" ftype="bigwig"/>
+            <param name="advancedOpt|showAdvancedOpt" value="yes"/>
+            <param name="mode|mode_select" value="scale-regions"/>
             <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size"/>
         </test>
     </tests>
diff --git a/galaxy/wrapper/computeMatrixOperations.xml b/galaxy/wrapper/computeMatrixOperations.xml
index d0b477b669..9d6413ed50 100755
--- a/galaxy/wrapper/computeMatrixOperations.xml
+++ b/galaxy/wrapper/computeMatrixOperations.xml
@@ -8,74 +8,80 @@
     <command>
 <![CDATA[
         @BINARY@
-            #if $submodule.command == "info":
-                info
-                -m $submodule.matrixFile
-                > $outFileTxt
-            #else if $submodule.command == "relabel":
-                relabel
-                -m $submodule.matrixFile
-                #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
-                    --groupLabels $submodule.groupLabels
-                #end if
-                #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
-                    --sampleLabels $submodule.sampleLabels
-                #end if
-            #else if $submodule.command == "subset":
-                subset
-                -m $submodule.matrixFile
-                #if $submodule.groups is not None and str($submodule.groups) != '':
-                    --groups $submodule.groups
-                #end if
-                #if $submodule.samples is not None and str($submodule.samples) != '':
-                    --samples $submodule.samples
-                #end if
-                -o $outFileName
-            #else if $submodule.command == "filterStrand":
-                filterStrand
-                -m $submodule.matrixFile
-                --strand $submodule.strand
-                -o $outFileName
-            #else if $submodule.command == "filterValues":
-                filterValues
-                -m $submodule.matrixFile
-                #if $submodule.minValue is not None and str($submodule.minValue) != '':
-                    --min $submodule.minValue
-                #end if
-                #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
-                    --max $submodule.maxValue
-                #end if
-                -o $outFileName
-            #else if $submodule.command == "rbind":
-                #set $files=[]
-                #for $f in $submodule.matrixFiles:
-                    #silent $files.append(str($f.matrixFile))
-                #end for
-                rbind
-                -m '#echo "' '".join($files)#'
-                -o $outFileName
-            #else if $submodule.command == "cbind":
-                cbind
-                #set $files=[]
-                #for $f in $submodule.matrixFiles:
-                    #silent $files.append(str($f.matrixFile))
-                #end for
-                -m '#echo "' '".join($files)#'
-                -o $outFileName
-            #else if $submodule.command == "sort":
-                sort
-                #set $files=[]
-                #for $f in $submodule.regionsFiles:
-                    #silent $files.append(str($f.regionsFile))
-                #end for
-                -m $submodule.matrixFile
-                -R '#echo "' '".join($files)#'
-                -o $outFileName
-            #else if $submodule.command == "dataRange":
-                dataRange
-                -m $submodule.matrixFile
-                > $outFileTxt
+        #if $submodule.command == "info":
+            info
+            -m '$submodule.matrixFile'
+        #else if $submodule.command == "relabel":
+            relabel
+            -m '$submodule.matrixFile'
+            #if $submodule.groupLabels:
+                --groupLabels '$submodule.groupLabels'
             #end if
+            #if $submodule.sampleLabels:
+                --sampleLabels '$submodule.sampleLabels'
+            #end if
+        #else if $submodule.command == "subset":
+            subset
+            -m '$submodule.matrixFile'
+            #if $submodule.groups:
+                --groups '$submodule.groups'
+            #end if
+            #if $submodule.samples:
+                --samples '$submodule.samples'
+            #end if
+        #else if $submodule.command == "filterStrand":
+            filterStrand
+            -m '$submodule.matrixFile'
+            #if $submodule.strand:
+                --strand '$submodule.strand'
+            #end if
+        #else if $submodule.command == "filterValues":
+            filterValues
+            -m '$submodule.matrixFile'
+            #if $submodule.min:
+                --min $submodule.min
+            #end if
+            #if $submodule.max:
+                --max $submodule.max
+            #end if
+        #else if $submodule.command == "rbind":
+            #set $files=[]
+            #for $f in $submodule.matrixFiles:
+                #silent $files.append(str($f.matrixFile))
+            #end for
+            rbind
+            -m '#echo "' '".join($files)#'
+        #else if $submodule.command == "cbind":
+            cbind
+            #set $files=[]
+            #for $f in $submodule.matrixFiles:
+                #silent $files.append(str($f.matrixFile))
+            #end for
+            -m '#echo "' '".join($files)#'
+        #else if $submodule.command == "sort":
+            sort
+            #set $files=[]
+            #for $f in $submodule.regionsFiles:
+                #silent $files.append(str($f.regionsFile))
+            #end for
+            -m '$submodule.matrixFile'
+            -R '#echo "' '".join($files)#'
+            #if $submodule.transcriptID:
+                --transcriptID '$submodule.transcriptID'
+            #end if
+            #if $submodule.transcript_id_designator:
+                --transcript_id_designator '$submodule.transcript_id_designator'
+            #end if
+        #else if $submodule.command == "dataRange":
+            dataRange
+            -m '$submodule.matrixFile'
+        #end if
+
+        #if $submodule.command == "info" or $submodule.command == "dataRange":
+            > '$outFileTxt'
+        #else:
+            -o '$outFileName'
+        #end if
 ]]>
     </command>
     <inputs>
@@ -92,11 +98,11 @@
                 <option value="dataRange">Returns the min, max, median, 10th and 90th percentile of the matrix values per sample (dataRange)</option>
             </param>
             <when value="info">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
             </when>
 
             <when value="relabel">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
                 <param argument="groupLabels" type="text" optional="true" label="New Region/Group Labels."
                     help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each group of regions."/>
                 <param argument="sampleLabels" type="text" optional="true" label="New Sample Labels."
@@ -104,7 +110,7 @@
             </when>
 
             <when value="subset">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
                 <param argument="groups" type="text" optional="true" label="Region groups to include."
                     help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)"/>
                 <param argument="samples" type="text" optional="true" label="Samples to include."
@@ -112,7 +118,7 @@
             </when>
 
             <when value="filterStrand">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
                 <param argument="--strand" type="select" label="Only include regions on this strand."
                     help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
                     <option value="+">+</option>
@@ -122,7 +128,7 @@
             </when>
 
             <when value="filterValues">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
                 <param argument="--min" type="float" optional="true" label="Minimum value"
                        help="Exclude any row in the matrix with a value below this. By default there is no minimum value."/>
                 <param argument="--max" type="float" optional="true" label="Maximum value"
@@ -131,26 +137,35 @@
 
             <when value="rbind">
                 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                    <expand macro="matrixFile" />
                 </repeat>
             </when>
 
             <when value="cbind">
                 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                    <expand macro="matrixFile" />
                 </repeat>
             </when>
 
             <when value="sort">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
                 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1">
                     <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
                         help="File, in BED format, containing the regions to plot."/>
                 </repeat>
+                <param argument="--transcriptID" optional="true" value="transcript" type="text"
+                    label="transcript designator"
+                    help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript"/>
+                <param argument="--transcript_id_designator" optional="true" value="transcript_id" type="text"
+                    label="transcriptID key designator"
+                    help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
+                        or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
+                        as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
+                        convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id"/>
             </when>
 
             <when value="dataRange">
-                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+                <expand macro="matrixFile" />
             </when>
         </conditional>
     </inputs>
@@ -158,30 +173,40 @@
         <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}">
             <filter>
             ((
-                submodule['command'] != "info"
+                submodule['command'] != "info" and submodule['command'] != "dataRange"
             ))
             </filter>
         </data>
         <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">
             <filter>
             ((
-                submodule['command'] == "info"
+                submodule['command'] == "info" or submodule['command'] == "dataRange"
             ))
             </filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="command" value="info"/>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
+            <param name="submodule|command" value="info"/>
+            <param name="submodule|matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
             <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="command" value="rbind"/>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
+            <param name="submodule|command" value="rbind"/>
+            <param name="submodule|matrixFiles_0|matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
+            <param name="submodule|matrixFiles_1|matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
             <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="submodule|command" value="dataRange"/>
+            <param name="submodule|matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive"/>
+            <output name="outFileTxt">
+                <assert_contents>
+                    <has_line_matching expression="Samples\tMin\tMax\tMedian\t10th\t90th"/>
+                    <has_line_matching expression="bamCoverage_result4_bw_0\t1122690.0\t5292690.0\t1884522.5\t1419407.0\t4410575.0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff --git a/galaxy/wrapper/correctGCBias.xml b/galaxy/wrapper/correctGCBias.xml
index b2293aaf34..8ce29a1ac3 100644
--- a/galaxy/wrapper/correctGCBias.xml
+++ b/galaxy/wrapper/correctGCBias.xml
@@ -27,9 +27,10 @@
                 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
             #end if
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
+            --binSize $binSize
             --correctedFile corrected.bam
 ]]>
     </command>
@@ -40,6 +41,11 @@
         <expand macro="reference_genome_source"/>
         <expand macro="effectiveGenomeSize"/>
         <expand macro="region_limit_operation"/>
+        <param argument="--binSize" type="integer" value="50" min="1"
+            label="Bin size in bases"
+            help="The genome will be divided into bins of the specified size. 
+                For each bin, the overlapping number of fragments (or reads) will be reported.
+                If only half a fragment overlaps then this fraction will be reported."/>
     </inputs>
     <outputs>
         <data format="bam" from_work_dir="corrected.bam" name="outFileName"/>
@@ -48,10 +54,10 @@
         <test expect_num_outputs="1">
             <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular"/>
             <param name="bamInput" value="paired_chr2L.bam" ftype="bam"/>
-            <param name="ref_source" value="history"/>
-            <param name="input1" value="sequence.2bit"/>
-            <param name="effectiveGenomeSize_opt" value="specific"/>
-            <param name="effectiveGenomeSize" value="10050"/>
+            <param name="source|ref_source" value="history"/>
+            <param name="source|input1" value="sequence.2bit"/>
+            <param name="effectiveGenomeSize|effectiveGenomeSize_opt" value="specific"/>
+            <param name="effectiveGenomeSize|effectiveGenomeSize" value="10050"/>
             <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="200"/>
         </test>
     </tests>
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 4246a18c45..1e2b9c13b5 100755
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -5,8 +5,8 @@
     <token name="@GALAXY_VERSION@">23.2</token>
     <xml name="requirements">
         <requirements>
-            <!-- <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement> -->
-            <requirement type="package" version="1.21">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
+            <requirement type="package" version="1.24">samtools</requirement>
         </requirements>
         <expand macro="stdio"/>
         <version_command>@BINARY@ --version</version_command>
@@ -26,8 +26,8 @@
     </xml>
 
     <token name="@PLOTWIDTHHEIGHT@">
-        --plotWidth '$advancedOpt.plotWidth'
-        --plotHeight '$advancedOpt.plotHeight'
+        --plotWidth $advancedOpt.plotWidth
+        --plotHeight $advancedOpt.plotHeight
     </token>
 
     <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
@@ -46,7 +46,6 @@
         #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
             --extendReads
         #end if
-        $advancedOpt.ignoreDuplicates
         $advancedOpt.centerReads
         #if $advancedOpt.minMappingQuality:
             --minMappingQuality $advancedOpt.minMappingQuality
@@ -68,13 +67,13 @@
     <token name="@ADVANCED_OPTS_GTF@">
         $advancedOpt.metagene
         #if $advancedOpt.transcriptID:
-            --transcriptID $advancedOpt.transcriptID
+            --transcriptID '$advancedOpt.transcriptID'
         #end if
         #if $advancedOpt.exonID:
-            --exonID $advancedOpt.exonID
+            --exonID '$advancedOpt.exonID'
         #end if
         #if $advancedOpt.transcript_id_designator:
-            --transcript_id_designator $advancedOpt.transcript_id_designator
+            --transcript_id_designator '$advancedOpt.transcript_id_designator'
         #end if
     </token>
 
@@ -86,10 +85,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -112,7 +111,7 @@
     </xml>
 
     <xml name="region_limit_operation">
-        <param argument="--region" type="text" value=""
+        <param argument="--region" type="text" value="" optional="true"
             label="Region of the genome to limit the operation to"
             help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
             <sanitizer>
@@ -126,93 +125,31 @@
     </xml>
 
     <xml name="smoothLength">
-        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
+        <param argument="--smoothLength" type="integer" value="" optional="true" min="1"
             label="Smooth values using the following length (in bases)"
             help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
     </xml>
 
-
-    <xml name="kmeans_clustering">
-        <conditional name="used_multiple_regions">
-            <param name="used_multiple_regions_options" type="select"
-                label="Did you compute the matrix with more than one groups of regions?"
-                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
-                <option value="yes">Yes, I used multiple groups of regions</option>
-                <option value="no">No, I used only one group</option>
-            </param>
-            <when value="no">
-                <conditional name="clustering">
-                    <param name="clustering_options" type="select" label="Clustering algorithm">
-                        <option value="none">No clustering</option>
-                        <option value="kmeans">Kmeans clustering</option>
-                        <option value="hclust">Hierarchical clustering</option>
-                    </param>
-                    <when value="kmeans">
-                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
-                            help="When this option is set, the matrix is split into clusters using the k-means algorithm.
-                            This only works for data that is not grouped, otherwise only the first group will be clustered.
-                            If more specific clustering methods are required it is advisable to save the underlying matrix and
-                            run the clustering using other software."/>
-                    </when>
-                    <when value="hclust">
-                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
-                            help="WARNING: This option causes the tool to run for a very long time! When this option is
-                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
-                            This only works for data that is not grouped, otherwise only the first group will be clustered.
-                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
-                            If more specific clustering methods are required it is advisable to save the underlying matrix and
-                            run the clustering using other software."/>
-                    </when>
-                    <when value="none"/>
-                </conditional>
-                <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
-                    label="Compute the silhouette score for each region"
-                    help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
-                    The silhouette score is a measure of how similar a region is to other regions in the same cluster as
-                    opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
-                    The silhouette evaluation can be very slow when you have more than 100 000 regions."/>
-            </when>
-            <when value="yes"/>
-        </conditional>
-    </xml>
-
-    <token name="@KMEANS_CLUSTERING@">
-        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
-            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
-                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
-                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
-                #end if
-            #end if
-            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
-                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
-                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
-                #end if
-            #end if
-            $advancedOpt.used_multiple_regions.silhouette
-        #end if
-    </token>
-
     <xml name="samFlags">
-        <param argument="--samFlagInclude" type="integer" optional="True" value=""
+        <param argument="--samFlagInclude" type="integer" optional="true" value=""
             label="Include reads based on the SAM flag"
             help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
-        <param argument="--samFlagExclude" type="integer" optional="True" value=""
+        <param argument="--samFlagExclude" type="integer" optional="true" value=""
             label="Exclude reads based on the SAM flag"
             help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
     </xml>
 
     <xml name="fragLength">
-        <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
+        <param argument="--minFragmentLength" type="integer" optional="true" value="0" min="0"
             label="Minimum fragment length for inclusion."
             help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments."/>
-        <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
+        <param argument="--maxFragmentLength" type="integer" optional="true" value="0" min="0"
             label="Maximum fragment length for inclusion."
             help="A value of 0 (the default) is equivalent to no maximum."/>
     </xml>
 
     <xml name="read_processing_options">
         <expand macro="extendReads"/>
-        <expand macro="ignoreDuplicates"/>
         <expand macro="centerReads"/>
         <expand macro="minMappingQuality"/>
         <expand macro="samFlags"/>
@@ -223,13 +160,13 @@
         <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
             label="Use a metagene model"
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored."/>
-        <param argument="--transcriptID" optional="True" value="transcript" type="text"
+        <param argument="--transcriptID" optional="true" value="transcript" type="text"
             label="transcript designator"
             help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript"/>
-        <param argument="--exonID" optional="True" value="exon" type="text"
+        <param argument="--exonID" optional="true" value="exon" type="text"
             label="exon designator"
             help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon"/>
-        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
+        <param argument="--transcript_id_designator" optional="true" value="transcript_id" type="text"
             label="transcriptID key designator"
             help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
                   or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
@@ -253,7 +190,7 @@
                      Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
                      Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
                      recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
-                <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
+                <option value="no" selected="true">No extension. The default value and most typically appropriate.</option>
                 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
                 <option value="custom">A custom length, which will be applied to ALL reads.</option>
             </param>
@@ -269,13 +206,13 @@
 
     <xml name="corMethod">
         <param argument="--corMethod" type="select" label="Correlation method">
-            <option value="spearman" selected="True">Spearman</option>
+            <option value="spearman" selected="true">Spearman</option>
             <option value="pearson">Pearson</option>
         </param>
     </xml>
 
-    <xml name="distanceBetweenBins">
-        <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
+    <xml name="distanceBetweenBins" tokens="DISTANCE">
+        <param argument="--distanceBetweenBins" type="integer" value="@DISTANCE@" min="0"
             label="Distance between bins"
             help="By default, multiBamSummary considers consecutive bins of
                 the specified 'Bin size'. However, to reduce the
@@ -307,6 +244,19 @@
             <option value="region_length">region length</option>
         </param>
     </xml>
+    
+    <xml name="sortUsingSamples">
+        <param argument="--sortUsingSamples" type="text"
+            label="List of samples to be used for sorting"
+            help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
+            If no value is set, it uses all samples. Example: 1 3 (space separated!)">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <add value=" "/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
 
     <xml name="sortRegionsComputeMatrix">
         <param argument="--sortRegions" type="select" label="Sort regions"
@@ -369,29 +319,67 @@
     <xml name="pseudocount">
         <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
-    <token name="@REFERENCES@">
 
-.. class:: infomark
+    <xml name="ggplot">
+        <param argument="--ggplot" type="boolean" truevalue="--ggplot" falsevalue=""
+            label ="Use ggplot theme for figures" />
+    </xml>
 
-For more information on the tools, please visit our `help site`_.
+    <xml name="region_file">
+        <param name="region_file" type="data" format="bed,gtf" 
+        label="Region file in BED or INTERVAL format"
+        help="Coverage is computed for the number of reads that overlap such regions."/>
+    </xml>
 
-For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
+    <xml name="outRawCounts">
+        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help="" />
+    </xml>
 
-This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+    <xml name="multiSummary_common_params">
+        <expand macro="custom_sample_labels" />
+        <conditional name="mode">
+            <param name="modeOpt" type="select" label="Choose computation mode"
+                help="In the bins mode, the correlation is computed using equally sized bins.
+                In the BED file mode, a list of genomic regions in BED format has to be given.
+                For each region in the BED file, the number of overlapping reads is counted in
+                each of the BAM/BigWig files. Then the correlation is computed.">
+                <option value="bins" selected="true">Bins</option>
+                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
+            </param>
+            <when value="bins">
+                <param name="binSize" type="integer" value="10000" min="1"
+                    label="Bin size in bp"
+                    help="Length in bases for a window used to sample the genome. (--binSize)"/>
 
-.. _Biostars: http://biostars.org
-.. _on github: http://github.com
-.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
-.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _help site: https://deeptools.readthedocs.org/
+                <expand macro="distanceBetweenBins" DISTANCE="0"/>
+            </when>
+            <when value="BED-file">
+                <expand macro="region_file" />
+            </when>
+        </conditional>
+        <expand macro="region_limit_operation" />
+        <expand macro="outRawCounts" />
+    </xml>
 
+    <token name="@MULTISUMMARY_COMMON_PARAMS@">
+        --outFileName '$outFile'
+        --labels #echo " ".join($labels)#
+
+        #if $outRawCounts:
+            --outRawCounts '$outFileRawCounts'
+        #end if
+
+        #if $mode.modeOpt == "bins":
+            --binSize $mode.binSize
+            --distanceBetweenBins $mode.distanceBetweenBins
+        #else:
+            --BED '$mode.region_file'
+        #end if
+
+        #if $region:
+            --region '$region'
+        #end if
     </token>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1093/nar/gkw257</citation>
-            <yield/>
-        </citations>
-    </xml>
 
     <xml name="multiple_input_bams" tokens="MIN">
         <conditional name="multibam_conditional">
@@ -432,57 +420,35 @@ is vital to you, select Yes below.">
         </conditional>
     </xml>
 
+
     <xml name="custom_sample_labels">
-	<conditional name="custom_sample_labels_conditional">
-        <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
-	    <option value="No" selected="true">No, use sample names in the history</option>
-	    <option value="Yes">Yes, I want to specify new labels</option>
-	</param>
-	<when value="No">
-	</when>
-	<when value="Yes">
-	    <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &apos;sample 1&apos;; &apos;sample 2&apos;)">
-            <sanitizer>
-                <valid initial="string.letters,string.digits,string.whitespace">
-                    <add value="&apos;"/>
-                    <add value="_"/>
-                </valid>
-            </sanitizer>
-            <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
-        </param>
-	</when>
-        </conditional>
+        <conditional name="custom_sample_labels_conditional">
+            <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
+                <option value="No" selected="true">No, use sample names in the history</option>
+                <option value="Yes">Yes, I want to specify new labels</option>
+            </param>
+            <when value="No">
+            </when>
+            <when value="Yes">
+                <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &apos;sample 1&apos;; &apos;sample 2&apos;)">
+                    <sanitizer>
+                        <valid initial="string.letters,string.digits,string.whitespace">
+                            <add value="&apos;"/>
+                            <add value="_"/>
+                        </valid>
+                    </sanitizer>
+                    <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
+                </param>
+            </when>
+            </conditional>
     </xml>
 
     <xml name="plotTitle">
-        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
+        <param argument="--plotTitle" type="text" value="" size="30" optional="true"
             label="Title of the plot"
             help="Title of the plot, to be printed on top of the generated image."/>
     </xml>
 
-    <xml name="legendLocation">
-        <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
-            <option value="best" selected="true">Best (automatic)</option>
-            <option value="upper-right">upper-right</option>
-            <option value="upper-left">upper-left</option>
-            <option value="upper-center">upper-center</option>
-            <option value="lower-right">lower-right</option>
-            <option value="lower-left">lower-left</option>
-            <option value="lower-center">lower-center</option>
-            <option value="center-right">center-right</option>
-            <option value="center-left">center-left</option>
-            <option value="center">center</option>
-            <option value="none">none (only works for heatmaps</option>
-        </param>
-    </xml>
-
-    <xml name="labelRotation">
-        <param argument="--labelRotation" type="integer" value="0"
-            label="Rotation of the X-axis labels (in degrees)"
-            help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation."/>
-    </xml>
-
-
     <token name="@multiple_input_bams@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
@@ -587,7 +553,12 @@ is vital to you, select Yes below.">
         #end for
         #if len($files) > 0:
             --BED #echo ' '.join($files)#
-            --regionLabels #echo ' '.join($labels)#
+            --regionLabels
+            #if $advancedOpt.regionLabels:
+                $advancedOpt.regionLabels
+            #else:
+                #echo ' '.join($labels)#
+            #end if
         #end if
 ]]>
     </token>
@@ -614,7 +585,7 @@ is vital to you, select Yes below.">
 
     <token name="@reference_genome_source@">
     #if $source.ref_source=="history":
-        --genome $source.input1
+        --genome '$source.input1'
     #else:
         --genome '$source.input1_2bit.fields.path'
     #end if
@@ -670,18 +641,6 @@ is vital to you, select Yes below.">
         </param>
     </xml>
 
-    <xml name="exactScaling">
-        <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
-            label="Compute an exact scaling factor"
-            help="Compute an exact scaling factor rather than one based on
-                  sampled reads. This is only useful in cases where you are
-                  filtering some alignments out AND this are both rare and
-                  tend to clump together in the genome. In such cases the
-                  region-based sampling employed by deepTools would produce
-                  inaccurate scaling factors. Note that this option results
-                  in the process taking significantly more time to complete."/>
-    </xml>
-
     <xml name="input_save_matrix_values">
         <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>
@@ -706,17 +665,16 @@ is vital to you, select Yes below.">
 
 
     <xml name="input_image_file_format">
-        <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
+        <param argument="--outFileFormat" type="select" label="Image file format">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
             <option value="svg">svg</option>
             <option value="eps">eps</option>
-            <option value="plotly">plotly</option>
         </param>
     </xml>
 
     <xml name="output_dpi">
-        <param argument="--dpi" type="integer" value="200" size="3" optional="True"
+        <param argument="--dpi" type="integer" value="200" size="3" optional="true"
             label="Image dpi" help=""/>
     </xml>
 
@@ -726,7 +684,6 @@ is vital to you, select Yes below.">
                 <when input="output.outFileFormat" value="pdf" format="pdf"/>
                 <when input="output.outFileFormat" value="svg" format="svg"/>
                 <when input="output.outFileFormat" value="eps" format="eps"/>
-                <when input="output.outFileFormat" value="plotly" format="html"/>
             </change_format>
         </data>
     </xml>
@@ -737,11 +694,14 @@ is vital to you, select Yes below.">
                 <when input="outFileFormat" value="pdf" format="pdf"/>
                 <when input="outFileFormat" value="svg" format="svg"/>
                 <when input="outFileFormat" value="eps" format="eps"/>
-                <when input="outFileFormat" value="plotly" format="html"/>
             </change_format>
         </data>
     </xml>
 
+    <xml name="matrixFile">
+        <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
+    </xml>
+    
     <xml name="output_save_matrix_values">
         <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
             <filter>
@@ -943,4 +903,189 @@ is vital to you, select Yes below.">
 
     </xml>
 
+    <xml name="no_collapse">
+        <param argument="--no_collapse" type="boolean" truevalue="--no_collapse" falsevalue="" checked="true"
+            label="Adjacent bins that have the same value are collapsed"
+            help="This reduces the size of the output file (drastically)"/>
+    </xml>
+
+
+    <token name="@HEATMAP_PROFILER_PARAMS@">
+        #if $advancedOpt.plotTitle:
+            --plotTitle '$advancedOpt.plotTitle'
+        #end if
+        $advancedOpt.perGroup
+        #if $advancedOpt.samplesLabel:
+            --samplesLabel '$advancedOpt.samplesLabel'
+        #end if
+        #if $advancedOpt.startLabel:
+            --startLabel '$advancedOpt.startLabel'
+        #end if
+        #if $advancedOpt.endLabel:
+            --endLabel '$advancedOpt.endLabel'
+        #end if
+        #if $advancedOpt.refPointLabel:
+            --refPointLabel '$advancedOpt.refPointLabel'
+        #end if
+          #if $advancedOpt.regionsLabel:
+            --regionsLabel '$advancedOpt.regionsLabel'
+        #end if
+        #if $advancedOpt.yMin:
+            --yMin $advancedOpt.yMin
+        #end if
+        #if $advancedOpt.yMax:
+            --yMax $advancedOpt.yMax
+        #end if
+        --legendLocation '$advancedOpt.legendLocation'
+        --labelRotation '$advancedOpt.labelRotation'
+        $advancedOpt.ggplot
+        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+                #end if
+            #end if
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+                #end if
+            #end if
+            $advancedOpt.used_multiple_regions.silhouette
+        #end if
+        #if $advancedOpt.clusterUsingSamples:
+            --clusterUsingSamples '$advancedOpt.clusterUsingSamples'
+        #end if
+    </token>
+
+    <xml name="heatmap_profiler_params">
+        <expand macro="plotTitle" />
+        <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
+            label="Make one plot per group of regions"
+            help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
+        <param argument="--samplesLabel" type="text"
+            label="Labels for the samples (each bigwig) plotted"
+            help="The default is to use the file name of the sample. The sample labels should be separated by
+            spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
+            <sanitizer>
+                <valid initial="string.printable">
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--startLabel" type="text" value="TSS" optional="true"
+            label="Label shown in the plot for the start of the region"
+            help ="Only for scale-regions mode. Default is TSS (transcription start site),
+            but could be changed to anything, e.g. &quot;peak start&quot;." />
+        <param argument="--endLabel" type="text" value="TES" optional="true"
+            label="Label shown in the plot for the region end"
+            help="Only for scale-regions mode. Default is TES (transcription end site)."/>
+        <param argument="--refPointLabel" type="text" optional="true" value=""
+            label="Label shown in the plot for the reference-point"
+            help ="only for reference-point mode. Default is the same as the reference point selected (e.g. TSS), 
+            but could be anything, e.g. &quot;peak start&quot; etc." />
+        <param argument="--regionsLabel" type="text"
+            label="Labels for the regions plotted in the heatmap"
+            help="If more than one region is being plotted a list of labels separated by space is required.
+                    If a label itself contains a space, then quotes are needed.
+                    For example, label_1 &quot;label 2&quot;" />
+
+        <param argument="--yMin" type="float" value="" optional="true"
+            label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
+        <param argument="--yMax" type="float" value="" optional="true"
+            label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
+        <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
+            <option value="best" selected="true">Best (automatic)</option>
+            <option value="upper-right">upper-right</option>
+            <option value="upper-left">upper-left</option>
+            <option value="upper-center">upper-center</option>
+            <option value="lower-right">lower-right</option>
+            <option value="lower-left">lower-left</option>
+            <option value="lower-center">lower-center</option>
+            <option value="center-right">center-right</option>
+            <option value="center-left">center-left</option>
+            <option value="center">center</option>
+            <option value="none">none (only works for heatmaps)</option>
+        </param>
+        <param argument="--labelRotation" type="integer" value="0"
+            label="Rotation of the X-axis labels (in degrees)"
+            help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation."/>
+        <expand macro="ggplot" />
+
+        <!--clustering params-->
+        <conditional name="used_multiple_regions">
+            <param name="used_multiple_regions_options" type="select"
+                label="Did you compute the matrix with more than one groups of regions?"
+                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
+                <option value="yes">Yes, I used multiple groups of regions</option>
+                <option value="no">No, I used only one group</option>
+            </param>
+            <when value="no">
+                <conditional name="clustering">
+                    <param name="clustering_options" type="select" label="Clustering algorithm">
+                        <option value="none">No clustering</option>
+                        <option value="kmeans">Kmeans clustering</option>
+                        <option value="hclust">Hierarchical clustering</option>
+                    </param>
+                    <when value="kmeans">
+                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
+                            help="When this option is set, the matrix is split into clusters using the k-means algorithm.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
+                            If more specific clustering methods are required it is advisable to save the underlying matrix and
+                            run the clustering using other software."/>
+                    </when>
+                    <when value="hclust">
+                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
+                            help="WARNING: This option causes the tool to run for a very long time! When this option is
+                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
+                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
+                            If more specific clustering methods are required it is advisable to save the underlying matrix and
+                            run the clustering using other software."/>
+                    </when>
+                    <when value="none"/>
+                </conditional>
+                <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
+                    label="Compute the silhouette score for each region"
+                    help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
+                    The silhouette score is a measure of how similar a region is to other regions in the same cluster as
+                    opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
+                    The silhouette evaluation can be very slow when you have more than 100 000 regions."/>
+            </when>
+            <when value="yes"/>
+        </conditional>
+        <param argument="--clusterUsingSamples" type="text"
+            label="List of samples to be used for clustering"
+            help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
+            If no value is set, it uses all samples. Example: 1 3 (space separated!)">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <add value=" "/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+
+    <token name="@REFERENCES@">
+
+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+.. _Biostars: http://biostars.org
+.. _on github: http://github.com
+.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://deeptools.readthedocs.org/
+
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gkw257</citation>
+            <yield/>
+        </citations>
+    </xml>
+
 </macros>
diff --git a/galaxy/wrapper/estimateReadFiltering.xml b/galaxy/wrapper/estimateReadFiltering.xml
index 925e8d0368..9d8d35ccb8 100644
--- a/galaxy/wrapper/estimateReadFiltering.xml
+++ b/galaxy/wrapper/estimateReadFiltering.xml
@@ -16,15 +16,15 @@
         --bamfiles #echo " ".join($files)#
         --sampleLabels #echo " ".join($labels)#
 
-        -bs '$binSize'
-        --distanceBetweenBins '$distanceBetweenBins'
+        -bs $binSize
+        --distanceBetweenBins $distanceBetweenBins
 
         #if str($filterRNAstrand) != 'no':
             --filterRNAstrand '$filterRNAstrand'
         #end if
         $ignoreDuplicates
         #if $minMappingQuality:
-            --minMappingQuality '$minMappingQuality'
+            --minMappingQuality $minMappingQuality
         #end if
         #if $samFlagInclude:
             --samFlagInclude $samFlagInclude
@@ -51,10 +51,7 @@
         <param name="binSize" type="integer" value="1000000" min="1"
             label="Bin size in bp"
             help="Length in bases of the window used to sample the genome. (--binSize)"/>
-        <param argument="--distanceBetweenBins" type="integer" value="10000" min="0"
-            label="Distance between bins"
-            help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased." />
-
+        <expand macro="distanceBetweenBins" DISTANCE="10000"/>
         <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
             help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                   Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
@@ -73,7 +70,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="bamfiles" value="paired_chr2L.bam,paired_chr2L.bam" ftype="bam" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="paired_chr2L.bam,paired_chr2L.bam" ftype="bam" />
             <param name="minMappingQuality" value="10" />
             <output name="outFileName" file="estimateReadFiltering.txt" ftype="tabular" />
         </test>
diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml
index c198a26020..b82700b873 100644
--- a/galaxy/wrapper/multiBamSummary.xml
+++ b/galaxy/wrapper/multiBamSummary.xml
@@ -12,78 +12,33 @@
 
         @multiple_input_bams@
         @BINARY@
-            $mode.modeOpt
-            @THREADS@
-
-            --outFileName '$outFile'
-            --bamfiles #echo " ".join($files)#
-            --labels #echo " ".join($labels)#
-
-            #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts'
-            #end if
-
-            #if $scalingFactors:
-                --scalingFactors '$scalingFactorsFile'
-            #end if
-
-            #if $mode.modeOpt == "bins":
-                --binSize '$mode.binSize'
-                --distanceBetweenBins '$mode.distanceBetweenBins'
-            #else:
-                --BED $mode.region_file
-            #end if
-
-            #if str($region).strip() != '':
-                --region '$region'
-            #end if
-
-            #if $advancedOpt.showAdvancedOpt == "yes":
-                @ADVANCED_OPTS_READ_PROCESSING@
-                @ADVANCED_OPTS_GTF@
-                @blacklist@
-            #end if
+        $mode.modeOpt
+        @THREADS@
+        --bamfiles #echo ' '.join($files)#
+
+        @MULTISUMMARY_COMMON_PARAMS@
+        
+        #if $scalingFactors:
+            --scalingFactors '$scalingFactorsFile'
+        #end if
+        
+        #if $advancedOpt.showAdvancedOpt == "yes":
+            @ADVANCED_OPTS_READ_PROCESSING@
+            @ADVANCED_OPTS_GTF@
+            @blacklist@
+        #end if
 ]]>
     </command>
 
     <inputs>
         <expand macro="multiple_input_bams" MIN="2"/>
-        <expand macro="custom_sample_labels" />
-
-        <conditional name="mode">
-            <param name="modeOpt" type="select" label="Choose computation mode"
-                    help="In the bins mode, the coverage is computed for equally
-                    sized bins. \nIn BED file mode, a list of genomic regions
-                    in BED or INTERVAL format has to be given. For each region
-                    in the BED file, the number of overlapping reads from each BAM file is counted.
-                    ">
-                <option value="bins" selected="true">Bins</option>
-                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
-            </param>
-            <when value="bins">
-                <param name="binSize" type="integer" value="10000" min="1"
-                    label="Bin size in bp"
-                    help="Length in bases of the window used to sample the genome. (--binSize)"/>
-
-                <expand macro="distanceBetweenBins" />
-
-            </when>
-            <when value="BED-file">
-                <param name="region_file" type="data" format="bed,gtf"
-                    label="Region file in BED or INTERVAL format"
-                    help="Coverage is computed for the number of reads that overlap such regions."/>
-            </when>
-        </conditional>
-
-        <expand macro="region_limit_operation" />
-
+        <expand macro="multiSummary_common_params" />
         <expand macro="advancedOpt_scaffold">
             <expand macro="read_processing_options" />
             <expand macro="gtf_options" />
             <expand macro="blacklist" />
         </expand>
 
-        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
         <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/>
 
     </inputs>
@@ -98,15 +53,17 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <param name="modeOpt" value="bins" />
-            <param name="binSize" value="10" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="mode|modeOpt" value="bins" />
+            <param name="mode|binSize" value="10" />
             <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
         <test expect_num_outputs="1">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <param name="modeOpt" value="BED-file" />
-            <param name="region_file" value="multiBamSummary_regions.bed" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="mode|modeOpt" value="BED-file" />
+            <param name="mode|region_file" value="multiBamSummary_regions.bed" />
             <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
 
diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/galaxy/wrapper/multiBigwigSummary.xml
index b63db25d58..be7488dc5a 100644
--- a/galaxy/wrapper/multiBigwigSummary.xml
+++ b/galaxy/wrapper/multiBigwigSummary.xml
@@ -12,66 +12,28 @@
 
         @multiple_input_bigwigs@
         @BINARY@
-            $mode.modeOpt
-
-            @THREADS@
-
-            --outFileName $outFile
-
-            --bwfiles #echo ' '.join($files)#
-
-            #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
-                --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
-            #end if
-            #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts'
-            #end if
-
-            #if $mode.modeOpt == "bins":
-                --binSize '$mode.binSize'
-                --distanceBetweenBins '$mode.distanceBetweenBins'
-            #else:
-                --BED $mode.region_file
-            #end if
-
-            #if str($region.value) != '':
-                --region '$region'
-            #end if
-
-            #if $advancedOpt.showAdvancedOpt == "yes":
-                @ADVANCED_OPTS_GTF@
-                @blacklist@
-            #end if
+        $mode.modeOpt
+        @THREADS@
+        --bwfiles #echo ' '.join($files)#
+
+        @MULTISUMMARY_COMMON_PARAMS@
+
+        #if $chromosomesToSkip.strip() != '':
+            --chromosomesToSkip '$chromosomesToSkip'
+        #end if
+        
+        #if $advancedOpt.showAdvancedOpt == "yes":
+            @ADVANCED_OPTS_GTF@
+            @blacklist@
+        #end if
 ]]>
     </command>
     <inputs>
         <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
-        <expand macro="custom_sample_labels" />
-
-        <conditional name="mode">
-            <param name="modeOpt" type="select" label="Choose computation mode"
-                help="In the bins mode, the correlation is computed using equally sized bins.
-                In the BED file mode, a list of genomic regions in BED format has to be given.
-                For each region in the BED file, the number of overlapping reads is counted in
-                each of the BigWig files. Then the correlation is computed.">
-                <option value="bins" selected="true">Bins</option>
-                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
-            </param>
-            <when value="bins">
-                <param name="binSize" type="integer" value="10000" min="1"
-                    label="Bin size in bp"
-                    help="Length in bases for a window used to sample the genome. (--binSize)"/>
-
-                <expand macro="distanceBetweenBins" />
-            </when>
-            <when value="BED-file">
-                <param name="region_file" type="data" format="bed,gtf"
-                    label="Region file in BED format"
-                    help="Correlation is computed for the number of reads that overlap such regions."/>
-            </when>
-        </conditional>
-        <expand macro="region_limit_operation" />
-        <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
+        <expand macro="multiSummary_common_params" />
+        <param argument="--chromosomesToSkip" type="text" value=""
+            label="Space separated list of chromosomes that you do not want to be included"
+            help="Useful to remove 'random' or 'extra' chr."/>
 
         <expand macro="advancedOpt_scaffold">
             <expand macro="gtf_options" />
@@ -87,15 +49,18 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
-            <param name="modeOpt" value="bins" />
-            <param name="binSize" value="10" />
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
+            <param name="mode|modeOpt" value="bins" />
+            <param name="mode|binSize" value="10" />
+            <param name="chromosomesToSkip" value="chr1 chr3" />
             <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
         <test expect_num_outputs="2">
-            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
-            <param name="modeOpt" value="bins" />
-            <param name="binSize" value="10" />
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
+            <param name="mode|modeOpt" value="bins" />
+            <param name="mode|binSize" value="10" />
             <param name="outRawCounts" value="True" />
             <conditional name="custom_sample_labels_conditional">
                 <param name="custom_labels_select" value="Yes"/>
@@ -104,6 +69,20 @@
             <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
             <output name="outFile" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
+        <test expect_num_outputs="2">
+            <param name="multibigwig_conditional|orderMatters" value="No" />
+            <param name="multibigwig_conditional|bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
+            <param name="mode|modeOpt" value="bins" />
+            <param name="mode|binSize" value="10" />
+            <param name="outRawCounts" value="True" />
+            <param name="chromosomesToSkip" value="chr1 chr3" />
+            <output name="outFileRawCounts" >
+                <assert_contents>
+                    <not_has_text text="chr1" />
+                    <not_has_text text="chr3" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml
index f15c8b819c..31b4364e0f 100644
--- a/galaxy/wrapper/plotCorrelation.xml
+++ b/galaxy/wrapper/plotCorrelation.xml
@@ -11,6 +11,9 @@
             --corData '$corData'
             --plotFile '$outFileName'
             --corMethod '$corMethod'
+            #if $custom_sample_labels_conditional.custom_labels_select == 'Yes':
+                --labels $custom_sample_labels_conditional.labels ## do not add quotes as the input might contain quotes
+            #end if
             --whatToPlot '$plotting_type.whatToPlot'
             #if str($plotting_type.whatToPlot) == 'heatmap':
                 @HEATMAP_OPTIONS@
@@ -32,16 +35,16 @@
             #if $outFileCorMatrix:
                 --outFileCorMatrix '$matrix'
             #end if
-
+            $ggplot
 ]]>
     </command>
     <inputs>
         <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>
         <expand macro="corMethod" />
-
+        <expand macro="custom_sample_labels" />
         <conditional name="plotting_type" >
             <param argument="--whatToPlot" type="select" label="Plotting type">
-                <option value="heatmap" selected="True">Heatmap</option>
+                <option value="heatmap" selected="true">Heatmap</option>
                 <option value="scatterplot">Scatterplot</option>
             </param>
             <when value="heatmap">
@@ -52,7 +55,7 @@
                 <expand macro="plotTitle" />
                 <conditional name="xrange_conditional">
                     <param type="select" name="xrange_select" label="Manually set X axis range?">
-                        <option value="no" selected="True">No</option>
+                        <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
@@ -65,7 +68,7 @@
                 </conditional>
                 <conditional name="yrange_conditional">
                     <param type="select" name="yrange_select" label="Manually set Y axis range?">
-                        <option value="no" selected="True">No</option>
+                        <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
@@ -100,6 +103,7 @@
                 unusually high counts."/>
 
         <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+        <expand macro="ggplot" />
 
     </inputs>
     <outputs>
@@ -112,17 +116,17 @@
         <test expect_num_outputs="2">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
-            <param name="outFileCorMatrix" value="True" />
+            <param name="outFileCorMatrix" value="true" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="2000" />
+            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
         <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
-            <param name="whatToPlot" value="scatterplot" />
-            <param name="removeOutliers" value="True" />
-            <param name="plotTitle" value="Test Plot" />
-            <output name="outFileName" file="plotCorrelation_result2.png" ftype="png" compare="sim_size" delta="2000" />
+            <param name="plotting_type|whatToPlot" value="scatterplot" />
+            <param name="removeOutliers" value="true" />
+            <param name="plotting_type|plotTitle" value="Test Plot" />
+            <output name="outFileName" file="plotCorrelation_result2.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
     </tests>
     <help>
diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml
index ee925b9a16..be59fc9d45 100644
--- a/galaxy/wrapper/plotCoverage.xml
+++ b/galaxy/wrapper/plotCoverage.xml
@@ -13,7 +13,6 @@
         @multiple_input_bams@
 
         @BINARY@
-
             @THREADS@
 
             --plotFile '$outFileName'
@@ -43,26 +42,24 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-                --numberOfSamples '$advancedOpt.numberOfSamples'
+                --numberOfSamples $advancedOpt.numberOfSamples
                 $advancedOpt.skipZeros
 
-                #if str($advancedOpt.region).strip() != '':
+                #if $advancedOpt.region:
                     --region '$advancedOpt.region'
                 #end if
-                --numberOfSamples $advancedOpt.numberOfSamples
 
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                #if $advancedOpt.plotTitle:
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
+                $advancedOpt.ggplot
                 @ADVANCED_OPTS_READ_PROCESSING@
                 @PLOTWIDTHHEIGHT@
                 @blacklist@
             #end if
-
 ]]>
     </command>
     <inputs>
-
         <expand macro="multiple_input_bams" MIN="1"/>
         <expand macro="custom_sample_labels" />
         <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
@@ -83,26 +80,20 @@
             </when>
         </conditional>
 
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
-                   label="Number of samples"
-                   help="Number of samples taken from the genome to compute the scaling factors."/>
-                <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
-                <expand macro="region_limit_operation" />
-                <expand macro="read_processing_options" />
-                <expand macro="skipZeros" />
-                <expand macro="plotTitle" />
-                <expand macro="blacklist" />
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <param argument="--numberOfSamples" type="integer" value="1000000" min="1"
+                label="Number of samples"
+                help="Number of samples taken from the genome to compute the scaling factors."/>
+            <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
+            <expand macro="region_limit_operation" />
+            <expand macro="read_processing_options" />
+            <expand macro="skipZeros" />
+            <expand macro="plotTitle" />
+            <expand macro="blacklist" />
+            <expand macro="ggplot" />
+        </expand>
         <expand macro="input_image_file_format" />
-        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
+        <expand macro="outRawCounts" />
     </inputs>
     <outputs>
         <expand macro="output_image_file_format_not_nested" />
@@ -115,24 +106,26 @@
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <!--param name="outFileFormat" value="png" /-->
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="plotTitle" value="Test Title from Galaxy" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|plotTitle" value="Test Title from Galaxy" />
             <param name="outRawCounts" value="True" />
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="9000" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
         <test expect_num_outputs="2">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="plotTitle" value="Test Title from Galaxy" />
-            <param name="showCoverageOpt" value="yes" />
-            <param name="coverageThreshold" value="0" />
-            <param name="coverageThreshold" value="5" />
-            <param name="coverageThreshold" value="10" />
-            <param name="coverageThreshold" value="20" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="9000" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|plotTitle" value="Test Title from Galaxy" />
+            <param name="coverageOpt|showCoverageOpt" value="yes" />
+            <param name="coverageOpt|thresholds_0|coverageThreshold" value="0" />
+            <param name="coverageOpt|thresholds_1|coverageThreshold" value="5" />
+            <param name="coverageOpt|thresholds_2|coverageThreshold" value="10" />
+            <param name="coverageOpt|thresholds_3|coverageThreshold" value="20" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="image_diff" eps="0.1" />
             <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
         </test>
     </tests>
diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml
index 265d150e5e..99575ca301 100644
--- a/galaxy/wrapper/plotEnrichment.xml
+++ b/galaxy/wrapper/plotEnrichment.xml
@@ -24,7 +24,7 @@
 
             --plotFileFormat '$outFileFormat'
 
-            #if str($region).strip() != "":
+            #if $region:
                 --region '$region'
             #end if
 
@@ -33,15 +33,11 @@
                     --attributeKey '$advancedOpt.attributeKey'
                 #end if
 
-                #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
-                    --labels $advancedOpt.labels
+                #if $advancedOpt.labels:
+                    --labels '$advancedOpt.labels'
                 #end if
 
-                #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
-                    --regionLabels $advancedOpt.regionLabels
-                #end if
-
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                #if $advancedOpt.plotTitle:
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
 
@@ -49,26 +45,22 @@
 
                 $advancedOpt.variableScales
 
-                $advancedOpt.perSample
-
-                $advancedOpt.variableScales
-
-                --plotWidth '$advancedOpt.plotWidth'
+                @PLOTWIDTHHEIGHT@
 
-                --plotHeight '$advancedOpt.plotHeight'
-
-                #if str($advancedOpt.colors).strip() != "":
+                #if $advancedOpt.colors:
                     --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                 #end if
 
-                --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
+                --numPlotsPerRow $advancedOpt.numPlotsPerRow
+
+                --alpha $advancedOpt.alpha
 
-                --alpha '$advancedOpt.alpha'
+                $advancedOpt.ggplot
 
                 @ADVANCED_OPTS_READ_PROCESSING@
 
                 #if $advancedOpt.Offset:
-                    --Offset $advancedOpt.Offset
+                    --Offset '$advancedOpt.Offset'
                 #end if
 
                 @blacklist@
@@ -93,13 +85,7 @@
                 attribute key. For example, the gene_biotype. Note that 'None' is used for BED files
                 or entries where the attributeKey is not found." />
 
-            <param argument="--plotHeight" type="integer" value="20" min="3"
-                label="Plot height"
-                help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
-
-            <param argument="--plotWidth" type="integer" value="20" min="1"
-                label="Plot width"
-                help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
+            <expand macro="plotWidthHeight" PLOTWIDTH="20" PLOTHEIGHT="20" />
 
             <param argument="--labels" type="text" size="30"
                 label="Labels for the samples (each BAM file) plotted"
@@ -141,13 +127,15 @@
                 label="Number of plots/row"
                 help="" />
 
+            <expand macro="ggplot" />
+
             <expand macro="read_processing_options" />
 
             <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
                 label="Include BED12 exons"
                 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
 
-            <param argument="--Offset" type="text"  value="" optional="True"
+            <param argument="--Offset" type="text"  value="" optional="true"
                 label="Offset inside each alignment to use for the signal location."
                 help="Uses this offset inside of each read as the signal. This is useful in
                     cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
@@ -162,10 +150,9 @@
                     is equivalent to trimming 4 bases from the 5-prime end of alignments." />
 
             <expand macro="blacklist" />
-
         </expand>
 
-        <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
+        <expand macro="outRawCounts" />
 
     </inputs>
     <outputs>
@@ -176,13 +163,14 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
             <param name="outRawCounts" value="true" />
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="minMappingQuality" value="0" />
-            <param name="regionLabels" value="up down" />
-            <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="5500" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|minMappingQuality" value="0" />
+            <param name="advancedOpt|regionLabels" value="up down" />
+            <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="image_diff" eps="0.1" />
             <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
         </test>
     </tests>
diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml
index 436e0c2ac6..79f349ccfa 100644
--- a/galaxy/wrapper/plotFingerprint.xml
+++ b/galaxy/wrapper/plotFingerprint.xml
@@ -10,13 +10,13 @@
         @multiple_input_bams@
         @BINARY@
             @THREADS@
-            --bamfiles #echo " ".join($files)
-            --labels #echo " ".join($labels)
-            --plotFile $outFileName
+            --bamfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
+            --plotFile '$outFileName'
 
             #if $output.showOutputSettings == "yes"
-                --plotFileFormat $output.outFileFormat
-                #if $output.saveRawCounts:
+                --plotFileFormat '$output.outFileFormat'
+                #if $output.outRawCounts:
                     --outRawCounts '$outFileRawCounts'
                 #end if
                 #if $output.saveQualityMetrics:
@@ -32,20 +32,20 @@
                 --plotFileFormat 'png'
             #end if
 
-            #if str($region).strip() != '':
+            #if $region:
                 --region '$region'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-                --binSize '$advancedOpt.binSize'
-                --numberOfSamples '$advancedOpt.numberOfSamples'
+                --binSize $advancedOpt.binSize
+                --numberOfSamples $advancedOpt.numberOfSamples
 
-                $advancedOpt.ignoreDuplicates
                 $advancedOpt.skipZeros
 
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                #if $advancedOpt.plotTitle:
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
+                $advancedOpt.ggplot
                 @ADVANCED_OPTS_READ_PROCESSING@
                 @blacklist@
             #end if
@@ -57,25 +57,19 @@
         <expand macro="custom_sample_labels" />
         <expand macro="region_limit_operation" />
 
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param argument="--binSize" type="integer" value="500" min="1"
-                   label="Bin size in bases"
-                   help="Length in bases for a window used to sample the genome."/>
-                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
-                   label="Number of samples"
-                   help="Number of samples taken from the genome to compute the scaling factors."/>
-                <expand macro="read_processing_options" />
-                <expand macro="skipZeros" />
-                <expand macro="plotTitle" />
-                <expand macro="blacklist" />
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <param argument="--binSize" type="integer" value="500" min="1"
+                label="Bin size in bases"
+                help="Length in bases for a window used to sample the genome."/>
+            <param argument="--numberOfSamples" type="integer" value="500000" min="1"
+                label="Number of samples"
+                help="Number of samples taken from the genome to compute the scaling factors."/>
+            <expand macro="read_processing_options" />
+            <expand macro="skipZeros" />
+            <expand macro="plotTitle" />
+            <expand macro="blacklist" />
+            <expand macro="ggplot" />
+        </expand>
 
         <conditional name="output">
             <param name="showOutputSettings" type="select" label="Show advanced output settings">
@@ -85,7 +79,7 @@
             <when value="no" />
             <when value="yes">
                 <expand macro="input_image_file_format" />
-                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
+                <expand macro="outRawCounts" />
                 <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
                    help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
                 <param name="JSDsample" type="data" format="bam" optional="true"
@@ -100,7 +94,7 @@
             <filter>
             ((
                 output['showOutputSettings'] == 'yes' and
-                output['saveRawCounts'] is True
+                output['outRawCounts'] is True
             ))
             </filter>
         </data>
@@ -115,20 +109,22 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <param name="showAdvancedOpt" value="no" />
-            <param name="showOutputSettings" value="no" />
-            <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="advancedOpt|showAdvancedOpt" value="no" />
+            <param name="output|showOutputSettings" value="no" />
+            <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
         <test expect_num_outputs="3">
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="showOutputSettings" value="yes" />
-            <param name="saveRawCounts" value="True" />
-            <param name="saveQualityMetrics" value="True" />
-            <param name="plotTitle" value="Test Fingerprint Plot" />
-            <param name="JSDsample" value="bowtie2 test1.bam" ftype="bam" />
-            <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" />
+            <param name="multibam_conditional|orderMatters" value="No" />
+            <param name="multibam_conditional|bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="output|showOutputSettings" value="yes" />
+            <param name="output|outRawCounts" value="true" />
+            <param name="output|saveQualityMetrics" value="true" />
+            <param name="advancedOpt|plotTitle" value="Test Fingerprint Plot" />
+            <param name="output|JSDsample" value="bowtie2 test1.bam" ftype="bam" />
+            <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="image_diff" eps="0.1" />
             <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" />
             <output name="outFileQualityMetrics" file="plotFingerprint_quality_metrics.tabular" ftype="tabular" />
         </test>
diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml
index de2fe68368..81a7f99ac5 100644
--- a/galaxy/wrapper/plotHeatmap.xml
+++ b/galaxy/wrapper/plotHeatmap.xml
@@ -28,6 +28,7 @@
             #else
                 --plotFileFormat 'png'
             #end if
+            --interpolationMethod '$interpolationMethod'
 
             #if $advancedOpt.showAdvancedOpt == "yes"
                 #if $advancedOpt.sortRegions:
@@ -60,29 +61,20 @@
                     --colorMap #echo " ".join($colorMap)#
                 #end if
 
-                --alpha '$advancedOpt.alpha'
-                #if str($advancedOpt.colorList).strip() != "":
-                    --colorList $advancedOpt.colorList
+                --alpha $advancedOpt.alpha
+                #if $advancedOpt.colorList:
+                    --colorList '$advancedOpt.colorList'
                 #end if
 
-                #if str($advancedOpt.zMin).strip() != "":
+                #if $advancedOpt.zMin:
                     --zMin $advancedOpt.zMin
                 #end if
-                #if str($advancedOpt.zMax).strip() != "":
+                #if $advancedOpt.zMax:
                     --zMax $advancedOpt.zMax
                 #end if
 
-                #if str($advancedOpt.yMin).strip() != "":
-                    --yMin $advancedOpt.yMin
-                #end if
-                #if str($advancedOpt.yMax).strip() != "":
-                    --yMax $advancedOpt.yMax
-                #end if
-                #if str($advancedOpt.sortUsingSamples).strip() != "":
-                    --sortUsingSamples $advancedOpt.sortUsingSamples
-                #end if
-                #if str($advancedOpt.clusterUsingSamples).strip() != "":
-                    --clusterUsingSamples $advancedOpt.clusterUsingSamples
+                #if $advancedOpt.sortUsingSamples:
+                    --sortUsingSamples '$advancedOpt.sortUsingSamples'
                 #end if
 
                 --xAxisLabel '$advancedOpt.xAxisLabel'
@@ -91,171 +83,95 @@
                 --heatmapWidth $advancedOpt.heatmapWidth
                 --heatmapHeight $advancedOpt.heatmapHeight
 
+                $advancedOpt.boxAroundHeatmaps
                 --whatToShow '$advancedOpt.whatToShow'
 
-                --startLabel '$advancedOpt.startLabel'
-                --endLabel '$advancedOpt.endLabel'
-
-                --refPointLabel '$advancedOpt.referencePointLabel'
-
-                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
-                    --samplesLabel $advancedOpt.samplesLabel
-                #end if
-
-                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
-                    --regionsLabel $advancedOpt.regionsLabel
-                #end if
-
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
-                    --plotTitle '$advancedOpt.plotTitle'
-                #end if
-
-                --legendLocation '$advancedOpt.legendLocation'
-
-                --labelRotation '$advancedOpt.labelRotation'
-
-                $advancedOpt.perGroup
-
-                @KMEANS_CLUSTERING@
-
+                @HEATMAP_PROFILER_PARAMS@
             #end if
 ]]>
     </command>
     <inputs>
-        <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
-               label="Matrix file from the computeMatrix tool" help=""/>
+        <expand macro="matrixFile" />
 
         <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
             <expand macro="output_dpi" />
             <expand macro="input_save_matrix_values" />
         </expand>
-
-        <conditional name="advancedOpt" >
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
+        <param argument="--interpolationMethod" type="select" label="Interpolation method for heatmap"
+            help="By default, plotHeatmap uses the method `nearest` if the number of columns is 1000 or less. See https://matplotlib.org/examples/images_contours_and_fields/interpolation_methods.html more info." >
+            <option value="auto" selected="true">auto</option>
+            <option value="nearest">nearest</option>
+            <option value="bilinear">bilinear</option>
+            <option value="bicubic">bicubic</option>
+            <option value="gaussian">gaussian</option>
+        </param>
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="sortRegions" />
+            <expand macro="sortUsing" />
+            <expand macro="sortUsingSamples" />
+            <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
+                label="Draw dashed lines in heatmap above all tick marks?" />
+            <param argument="--averageTypeSummaryPlot" type="select"
+                label="Type of statistic that should be plotted in the summary image above the heatmap"
+                help="">
+                <option value="mean" selected="true">mean</option>
+                <option value="median">median</option>
+                <option value="min">min</option>
+                <option value="max">max</option>
+                <option value="sum">sum</option>
+                <option value="std">std</option>
+            </param>
+            <param argument="--plotType" type="select" label="Type of summary plot">
+                <option value="lines">plot the profile line based on the statistic selected above.</option>
+                <option value="fill">fills the region between zero and the profile.</option>
+                <option value="se">color the region between the profile and the standard error.</option>
+                <option value="std">color the region between the profile and the standard deviation.</option>
+            </param>
+            <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
+                help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
+                By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
+                Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
+                Alternatively colors can be specified using the #rrggbb notation." />
+
+            <repeat name="colorMapRepeat" title="Colormap to use for each sample"
+                help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
+                <expand macro="colorMap" />
+            </repeat>
+            <param argument="--alpha" type="float" value="1.0" min="0.0"
+                max="1.0" optional="true"
+                label="Alpha channel (transparency)"
+                help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
+                be between 0 and 1. A value of 0.0 would be fully transparent." />
+
+            <param argument="--colorList" type="text" value="" optional="true"
+                label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
+                help="The color of the heatmaps can be specified as a list of colors separated by comas with
+                not space in between. For example: white,blue white,green will set a color map from white
+                to blue for the first heatmap and for white to green for the next heatmap."/>
+            <expand macro="zMin_zMax" />
+            <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)"
+                label="The x-axis label" help="" />
+            <param argument="--yAxisLabel" type="text" value="genes"
+                label="The y-axis label for the top panel" help="" />
+
+            <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
+                label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
+            <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
+                label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
+
+            <param argument="--boxAroundHeatmaps" type="boolean" truevalue="--boxAroundHeatmaps" falsevalue="" checked="true"
+                label="Plot black boxes around the heatmaps" help="The default is to not plot black boxes around the heatmaps. Choosing this option will plot black boxes around the heatmaps."/>
+
+            <param argument="--whatToShow" type="select" label="What to show"
+                help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
+                <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
+                <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
+                <option value="heatmap and colorbar">heatmap and colorbar</option>
             </param>
-            <when value="no" />
-            <when value="yes">
-                <expand macro="sortRegions" />
-                <expand macro="sortUsing" />
-                <param argument="--sortUsingSamples" type="text"
-                    label="List of samples to be used for sorting"
-                    help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                            <add value=" "/>
-                        </valid>
-                    </sanitizer>
-                </param>
-                <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
-                    label="Draw dashed lines in heatmap above all tick marks?" />
-                <param argument="--averageTypeSummaryPlot" type="select"
-                    label="Type of statistic that should be plotted in the summary image above the heatmap"
-                    help="">
-                    <option value="mean" selected="true">mean</option>
-                    <option value="median">median</option>
-                    <option value="min">min</option>
-                    <option value="max">max</option>
-                    <option value="sum">sum</option>
-                    <option value="std">std</option>
-                </param>
-                <param argument="--plotType" type="select" label="Type of summary plot">
-                    <option value="lines">plot the profile line based on the statistic selected above.</option>
-                    <option value="fill">fills the region between zero and the profile.</option>
-                    <option value="se">color the region between the profile and the standard error.</option>
-                    <option value="std">color the region between the profile and the standard deviation.</option>
-                </param>
-                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
-                    help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
-                    By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
-                    Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
-                    Alternatively colors can be specified using the #rrggbb notation." />
-
-                <repeat name="colorMapRepeat" title="Colormap to use for each sample"
-                    help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
-                    <expand macro="colorMap" />
-                </repeat>
-                <param argument="--alpha" type="float" value="1.0" min="0.0"
-                    max="1.0" optional="True"
-                    label="Alpha channel (transparency)"
-                    help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
-                    be between 0 and 1. A value of 0.0 would be fully transparent." />
-
-                <param argument="--colorList" type="text" value="" optional="True"
-                    label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
-                    help="The color of the heatmaps can be specified as a list of colors separated by comas with
-                    not space in between. For example: white,blue white,green will set a color map from white
-                    to blue for the first heatmap and for white to green for the next heatmap."/>
-                <expand macro="zMin_zMax" />
-                <param argument="--yMin" type="float" value="" optional="True"
-                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
-                <param argument="--yMax" type="float" value="" optional="True"
-                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
-                <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)"
-                    label="The x-axis label" help="" />
-                <param argument="--yAxisLabel" type="text" value="genes"
-                    label="The y-axis label for the top panel" help="" />
-
-                <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
-                    label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
-                <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
-                    label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
-
-                <param argument="--whatToShow" type="select" label="What to show"
-                    help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
-                    <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
-                    <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
-                    <option value="heatmap and colorbar">heatmap and colorbar</option>
-                </param>
-
-                <param argument="--startLabel" type="text" value="TSS"
-                    label="Label for the region start"
-                    help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
-                <param argument="--endLabel" type="text" value="TES"
-                    label="Label for the region end"
-                    help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-
-                <param argument="--referencePointLabel" type="text" value="TSS"
-                    label="Reference point label"
-                    help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
-                <param argument="--samplesLabel" type="text"
-                    label="Labels for the samples (each bigwig) plotted"
-                    help="The default is to use the file name of the sample. The sample labels should be separated by
-                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                        </valid>
-                    </sanitizer>
-                </param>
-                <param argument="--regionsLabel" type="text"
-                    label="Labels for the regions plotted in the heatmap"
-                    help="If more than one region is being plotted a list of labels separated by space is required.
-                          If a label itself contains a space, then quotes are needed.
-                          For example, label_1 &quot;label 2&quot;" />
-
-                <expand macro="plotTitle" />
-                <expand macro="legendLocation" />
-                <expand macro="labelRotation" />
-                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
-                    label="Make one plot per group of regions"
-                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>
-
-                <expand macro="kmeans_clustering" />
-                <param argument="--clusterUsingSamples" type="text"
-                    label="List of samples to be used for clustering"
-                    help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                            <add value=" "/>
-                        </valid>
-                    </sanitizer>
-                </param>
-            </when>
-        </conditional>
+
+            <expand macro="heatmap_profiler_params" />
+        </expand>
     </inputs>
     <outputs>
         <expand macro="output_image_file_format" />
@@ -265,13 +181,19 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
-            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="10000" />
+            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="image_diff" eps="0.1" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|boxAroundHeatmaps" value="false" />
+            <param name="advancedOpt|whatToShow" value="heatmap and colorbar" />
+            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
         <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="whatToShow" value="heatmap and colorbar" />
-            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="11000" />
+            <param name="interpolationMethod" value="gaussian" />
+            <output name="outFileName" file="heatmapper_result3.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
     </tests>
     <help>
diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
index f5fe600e88..b505e479d9 100644
--- a/galaxy/wrapper/plotPCA.xml
+++ b/galaxy/wrapper/plotPCA.xml
@@ -10,6 +10,9 @@
         @BINARY@
             --corData '$corData'
             --plotTitle '$plotTitle'
+            #if $custom_sample_labels_conditional.custom_labels_select == 'Yes':
+                --labels $custom_sample_labels_conditional.labels ## do not add quotes as the input might contain quotes
+            #end if
             --plotFile '$outFileName'
             --plotFileFormat '$outFileFormat'
             #if str($advancedOpt.showAdvancedOpt) == 'yes':
@@ -20,13 +23,15 @@
                 $advancedOpt.transpose
                 $advancedOpt.rowCenter
                 #if $advancedOpt.colors:
-                    --colors $advancedOpt.colors
+                    --colors '$advancedOpt.colors'
                 #end if
                 #if $advancedOpt.markers:
-                    --markers $advancedOpt.markers
+                    --markers '$advancedOpt.markers'
                 #end if
+                $advancedOpt.addLabels
+                $advancedOpt.ggplot
             #end if
-            #if $outFileNameData
+            #if $outFileNameData:
                 --outFileNameData '$output_outFileNameData'
             #end if
 ]]>
@@ -35,28 +40,26 @@
         <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
         <expand macro="input_image_file_format" />
         <expand macro="plotTitle" />
+        <expand macro="custom_sample_labels" />
         <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
-                <param argument="--PCs" label="Principal components to plot" value="1 2" type="text"
-                    help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
-                <param argument="--ntop" label="Number of rows to use" value="1000" type="integer"
-                    help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
-                <param argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
-                <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
-                <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
-                <param argument="--colors" type="text" label="Symbol colors" value="" optional="True"
-                    help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
-                <param argument="--markers" type="text" label="Custom markers" value="" optional="True"
-                    help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
-            </when>
-        </conditional>
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="plotWidthHeight" PLOTWIDTH="12.0" PLOTHEIGHT="10.0" />
+            <param argument="--PCs" label="Principal components to plot" value="1 2" type="text"
+                help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
+            <param argument="--ntop" label="Number of rows to use" value="1000" type="integer"
+                help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
+            <param argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
+            <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
+            <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
+            <param argument="--colors" type="text" label="Symbol colors" value="" optional="true"
+                help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
+            <param argument="--markers" type="text" label="Custom markers" value="" optional="true"
+                help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
+            <param argument="--addLabels" type="boolean" label="Add Labels to the plot" 
+                help="If specified, the labels will be added next to points also legend is omitted." 
+                truevalue="--addLabels" falsevalue="" />
+            <expand macro="ggplot" />
+        </expand>
     </inputs>
     <outputs>
         <expand macro="output_image_file_format_not_nested" />
@@ -69,15 +72,15 @@
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
-            <param name="showAdvancedOpt" value="yes" />
-            <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
         <test expect_num_outputs="2">
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
-            <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
+            <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="image_diff" eps="0.1" />
             <output name="output_outFileNameData" ftype="tabular">
                 <!-- The duplicate-sample column is mathematically zero, so it comes
                      out as tiny BLAS-dependent noise (~1e-18) that varies across
@@ -87,7 +90,7 @@
                 <assert_contents>
                     <has_n_columns n="4" />
                     <has_line_matching expression="Component\tbowtie2-test1.bam\tbowtie2-test1.bam\tEigenvalue" />
-                    <has_line_matching expression="1\t-?1\.99949\d*\t.*\t2\.9999\d*" />
+                    <has_line_matching expression="1\t-?1\.99949\d*\t.*\t2\.999\d*" />
                     <has_line_matching expression="2\t-?0\.96079\d*\t.*" />
                 </assert_contents>
             </output>
diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml
index ff7d7d07b0..bf1b16281d 100644
--- a/galaxy/wrapper/plotProfiler.xml
+++ b/galaxy/wrapper/plotProfiler.xml
@@ -14,7 +14,7 @@
             --outFileName "$outFileName"
 
             #if $output.showOutputSettings == "yes"
-                --plotFileFormat $output.outFileFormat
+                --plotFileFormat '$output.outFileFormat'
 
                 #if $output.dpi:
                     --dpi '$output.dpi'
@@ -27,162 +27,77 @@
                 --plotFileFormat 'png'
             #end if
 
-            #if $scaleRegions.showScaleRegionsOpt == "yes":
-                --startLabel '$scaleRegions.startLabel'
-                --endLabel '$scaleRegions.endLabel'
-            #end if
-
             #if $advancedOpt.showAdvancedOpt == "yes":
                 #if $advancedOpt.averageType:
                     --averageType '$advancedOpt.averageType'
                 #end if
-                --plotHeight $advancedOpt.plotHeight
-                --plotWidth $advancedOpt.plotWidth
-                --plotType $advancedOpt.plotType
-                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
-                    --samplesLabel $advancedOpt.samplesLabel
-                #end if
-
-                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
-                    --regionsLabel $advancedOpt.regionsLabel
-                #end if
-
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
-                    --plotTitle '$advancedOpt.plotTitle'
-                #end if
+                @PLOTWIDTHHEIGHT@
+                --plotType '$advancedOpt.plotType'
 
                 #if str($advancedOpt.colors).strip() != "":
                     --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                 #end if
 
-                --legendLocation '$advancedOpt.legendLocation'
-
-                --labelRotation '$advancedOpt.labelRotation'
-
-                $advancedOpt.perGroup
-
-                #if str($advancedOpt.yMin):
-                    --yMin $advancedOpt.yMin
-                #end if
-                #if str($advancedOpt.yMax):
-                    --yMax $advancedOpt.yMax
-                #end if
+                --numPlotsPerRow $advancedOpt.numPlotsPerRow
 
                 #if $advancedOpt.outFileNameData:
                     --outFileNameData '$output_outFileNameData'
                 #end if
 
-                @KMEANS_CLUSTERING@
+                @HEATMAP_PROFILER_PARAMS@
 
             #end if
 ]]>
     </command>
     <inputs>
-        <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
-        <conditional name="scaleRegions">
-            <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param argument="--startLabel" type="text" value="TSS" size="10"
-                    label="Label for the region start"
-                    help ="Label shown in the plot
-                    for the start of the region. Default is TSS (transcription start site),
-                    but could be changed to anything, e.g. &quot;peak start&quot;." />
-                <param argument="--endLabel" type="text" value="TES" size="10"
-                    label="Label for the region end"
-                    help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-            </when>
-        </conditional>
+        <expand macro="matrixFile" />
 
         <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
             <expand macro="output_dpi" />
         </expand>
 
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
+        <expand macro="advancedOpt_scaffold">
+            <expand macro="heatmap_profiler_params" />
+            <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
+                <option value="mean" selected="true">mean</option>
+                <option value="median">median</option>
+                <option value="min">min</option>
+                <option value="max">max</option>
+                <option value="sum">sum</option>
+                <option value="std">std</option>
+            </param>
+            <expand macro="plotWidthHeight" PLOTWIDTH="7.0" PLOTHEIGHT="11.0" />
+
+            <param argument="--plotType" type="select" label="Plot type"
+                help="The &quot;lines&quot; option will
+                plot the profile line based on the average type selected. The &quot;fill&quot;
+                option fills the region between zero and the profile curve. The filled in color is
+                semi-transparent. The &quot;add standard error&quot;
+                option colors the region between the profile and the standard error of the data.
+                As in the case of fill, a semi-transparent color is used.
+                The option &quot;overlapped_lines&quot; plots each region's value, one on top of
+                the other.">
+                <option value="lines" selected="true">lines</option>
+                <option value="fill">fill</option>
+                <option value="se">add standard error</option>
+                <option value="std">add standard deviation</option>
+                <option value="overlapped_lines">overlapped lines</option>
+                <option value="heatmap">heatmap</option>
             </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
-                    <option value="mean" selected="true">mean</option>
-                    <option value="median">median</option>
-                    <option value="min">min</option>
-                    <option value="max">max</option>
-                    <option value="sum">sum</option>
-                    <option value="std">std</option>
-                </param>
-                <param argument="--plotHeight" type="integer" value="5" min="3"
-                    label="Plot height"
-                    help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
-
-                <param argument="--plotWidth" type="integer" value="11" min="1"
-                    label="Plot width"
-                    help="Width in cm. The default value is 11 centimeters. The minimum value is 1 cm." />
-
-                <param argument="--plotType" type="select" label="Plot type"
-                    help="The &quot;lines&quot; option will
-                    plot the profile line based on the average type selected. The &quot;fill&quot;
-                    option fills the region between zero and the profile curve. The filled in color is
-                    semi-transparent. The &quot;add standard error&quot;
-                    option colors the region between the profile and the standard error of the data.
-                    As in the case of fill, a semi-transparent color is used.
-                    The option &quot;overlapped_lines&quot; plots each region's value, one on top of
-                    the other.">
-                    <option value="lines" selected="true">lines</option>
-                    <option value="fill">fill</option>
-                    <option value="se">add standard error</option>
-                    <option value="std">add standard deviation</option>
-                    <option value="overlapped_lines">overlapped lines</option>
-                    <option value="heatmap">heatmap</option>
-                </param>
-                <param argument="--samplesLabel" type="text" size="30"
-                    label="Labels for the samples (each bigwig) plotted"
-                    help="The default is to use the file name of the sample. The sample labels should be separated by
-                    spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                        </valid>
-                    </sanitizer>
-                </param>
-                <param argument="--regionsLabel" type="text" size="30"
-                    label="Labels for the regions plotted in the heatmap"
-                    help="If more than one region is being plotted a list of labels separated by space is required.
-                          If a label itself contains a space, then quotes are needed.
-                          For example, label_1 &quot;label 2&quot;" />
-
-                <expand macro="plotTitle" />
-                <param argument="--colors" type="text" value="" size="40"
-                    label="List of colors to use for the plotted lines"
-                    help="Color names and html hex strings (e.g. #eeff22) are accepted.
-                    The color names should be separated by spaces. (--colors red blue green)">
-                    <validator type="expression"
-                        message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
-                </param>
-                <expand macro="legendLocation" />
-                <expand macro="labelRotation" />
-
-                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
-                    label="Make one plot per group of regions"
-                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
-
-                <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile"
-                    help="This option will create an additional output file." />
-
-                <param argument="--yMin" type="float" value="" size="3" optional="true"
-                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
-                <param argument="--yMax" type="float" value="" size="3" optional="true"
-                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
-
-                <expand macro="kmeans_clustering" />
-
-            </when>
-        </conditional>
+            <param argument="--colors" type="text" value="" size="40"
+                label="List of colors to use for the plotted lines"
+                help="Color names and html hex strings (e.g. #eeff22) are accepted.
+                The color names should be separated by spaces. (--colors red blue green)">
+                <validator type="expression"
+                    message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
+            </param>
+            <param argument="--numPlotsPerRow" type="integer" value="8" min="1"
+                label="Number of plots per row" help="" />
+
+            <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile"
+                help="This option will create an additional output file." />
+        </expand>
     </inputs>
     <outputs>
         <expand macro="output_image_file_format" />
@@ -194,17 +109,20 @@
 
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
-            <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
-        </test>
         <test expect_num_outputs="2">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
-            <param name="showAdvancedOpt" value="yes" />
-            <param name="showScaleRegionsOpt" value="yes" />
-            <param name="outFileNameData" value="True" />
-            <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
-            <output name="output_outFileNameData" file="profiler_result2.tabular" ftype="tabular" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|outFileNameData" value="True" />
+            <param name="advancedOpt|startLabel" value="TSS" />
+            <param name="advancedOpt|endLabel" value="TES" />
+            <output name="outFileName" file="profiler_result1.png" ftype="png" compare="image_diff" eps="0.1" />
+            <output name="output_outFileNameData" file="profiler_result1.tabular" ftype="tabular" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="matrixFile" value="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" />
+            <param name="advancedOpt|showAdvancedOpt" value="yes" />
+            <param name="advancedOpt|refPointLabel" value="REF" />
+            <output name="outFileName" file="profiler_result2.png" ftype="png" compare="image_diff" eps="0.1" />
         </test>
     </tests>
     <help>
diff --git a/galaxy/wrapper/test-data/bigwigCompare_result3.bg b/galaxy/wrapper/test-data/bigwigCompare_result3.bg
new file mode 100644
index 0000000000..aec1418a7c
--- /dev/null
+++ b/galaxy/wrapper/test-data/bigwigCompare_result3.bg
@@ -0,0 +1,120 @@
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+ch1	350	360	1
+ch1	360	370	1
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+ch1	390	400	1
+ch2	0	10	1
+ch2	10	20	1
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+ch2	320	330	1
+ch2	330	340	1
+ch2	340	350	1
+ch2	350	360	1
+ch2	360	370	1
+ch2	370	380	1
+ch2	380	390	1
+ch2	390	400	1
+ch3	0	10	1
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+ch3	20	30	1
+ch3	30	40	1
+ch3	40	50	1
+ch3	50	60	1
+ch3	60	70	1
+ch3	70	80	1
+ch3	80	90	1
+ch3	90	100	1
+ch3	100	110	1
+ch3	110	120	1
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+ch3	140	150	1
+ch3	150	160	1
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+ch3	190	200	1
+ch3	200	210	1
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+ch3	220	230	1
+ch3	230	240	1
+ch3	240	250	1
+ch3	250	260	1
+ch3	260	270	1
+ch3	270	280	1
+ch3	280	290	1
+ch3	290	300	1
+ch3	300	310	1
+ch3	310	320	1
+ch3	320	330	1
+ch3	330	340	1
+ch3	340	350	1
+ch3	350	360	1
+ch3	360	370	1
+ch3	370	380	1
+ch3	380	390	1
+ch3	390	400	1
diff --git a/galaxy/wrapper/test-data/heatmapper_result1.png b/galaxy/wrapper/test-data/heatmapper_result1.png
index 79ea48ccdb..8ed1123eb9 100644
Binary files a/galaxy/wrapper/test-data/heatmapper_result1.png and b/galaxy/wrapper/test-data/heatmapper_result1.png differ
diff --git a/galaxy/wrapper/test-data/heatmapper_result2.png b/galaxy/wrapper/test-data/heatmapper_result2.png
index 8f85dfcbca..86f251f433 100644
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diff --git a/galaxy/wrapper/test-data/heatmapper_result3.png b/galaxy/wrapper/test-data/heatmapper_result3.png
new file mode 100644
index 0000000000..c93a3d9f4d
Binary files /dev/null and b/galaxy/wrapper/test-data/heatmapper_result3.png differ
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.png b/galaxy/wrapper/test-data/plotCorrelation_result1.png
index 3e03857308..e1261a6c7a 100644
Binary files a/galaxy/wrapper/test-data/plotCorrelation_result1.png and b/galaxy/wrapper/test-data/plotCorrelation_result1.png differ
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result2.png b/galaxy/wrapper/test-data/plotCorrelation_result2.png
index d649de236d..37add07f94 100644
Binary files a/galaxy/wrapper/test-data/plotCorrelation_result2.png and b/galaxy/wrapper/test-data/plotCorrelation_result2.png differ
diff --git a/galaxy/wrapper/test-data/plotCoverage_result1.png b/galaxy/wrapper/test-data/plotCoverage_result1.png
index 2995090986..d64b85de4a 100644
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diff --git a/galaxy/wrapper/test-data/plotEnrichment_output.png b/galaxy/wrapper/test-data/plotEnrichment_output.png
index 6ff056e0b2..0af0c079ce 100644
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diff --git a/galaxy/wrapper/test-data/plotFingerprint_result1.png b/galaxy/wrapper/test-data/plotFingerprint_result1.png
index 792763381d..556779c323 100644
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diff --git a/galaxy/wrapper/test-data/plotFingerprint_result2.png b/galaxy/wrapper/test-data/plotFingerprint_result2.png
index a9f4ca5523..6da4e1b868 100644
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diff --git a/galaxy/wrapper/test-data/plotPCA_result1.png b/galaxy/wrapper/test-data/plotPCA_result1.png
index b043d20f58..92eba0fba7 100644
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diff --git a/galaxy/wrapper/test-data/plotPCA_result2.png b/galaxy/wrapper/test-data/plotPCA_result2.png
index 1f4338467c..92eba0fba7 100644
Binary files a/galaxy/wrapper/test-data/plotPCA_result2.png and b/galaxy/wrapper/test-data/plotPCA_result2.png differ
diff --git a/galaxy/wrapper/test-data/profiler_result1.png b/galaxy/wrapper/test-data/profiler_result1.png
index 2cdfba2255..64e8efaf46 100644
Binary files a/galaxy/wrapper/test-data/profiler_result1.png and b/galaxy/wrapper/test-data/profiler_result1.png differ
diff --git a/galaxy/wrapper/test-data/profiler_result1.tabular b/galaxy/wrapper/test-data/profiler_result1.tabular
new file mode 100644
index 0000000000..c6cab1174c
--- /dev/null
+++ b/galaxy/wrapper/test-data/profiler_result1.tabular
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1.0	2.0
+bamCoverage_result4_bw_0	genes	2477942.875	2610260.125
diff --git a/galaxy/wrapper/test-data/profiler_result2.png b/galaxy/wrapper/test-data/profiler_result2.png
index 445da93b84..ec79134f5a 100644
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