chore: Update the Galaxy wrappers - #1465

Merged

WardDeb merged 35 commits into

deeptools:masterfrom

pavanvidem:gxy-4

Sep 13, 2026

Commits on Sep 8, 2026

Commits on Sep 9, 2026

testing an obsolete param
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59af6ef
use *_old binaries
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e651df5

Commits on Sep 10, 2026

revert old binary usage
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93704d1
remove --ignoreDuplicates from bamCoverage, bamCompare, multiBamSummary, plotCoverage, plotFingerprint and plotEnrichment
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aff01a6
Remove --exactScaling entirely
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09c0032
Remove SES option for --scaleFactorsMethod, --sampleLength and --numberOfSamples params
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094bf3f
Remove plotly inputs and outputs everywhere
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2e6b71e
Remove --plotTitle from bigwigCompare
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e48dc0f
add --no_collapse option and include it in tests
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2f95e16
add --sortUsingSamples to computeMatrix
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d3ade57
add --chromosomesToSkip and a test to multiBigwigSummary
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3a832f3
add --fixedStep param and a test to bigwigCompare
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eec5492
add --boxAroundHeatmaps param and a test to plotHeatmap
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e093d10
add fixedStep commandline
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12756f9
add --ggplot param
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6924c72
add --interpolationMethod to plotHeatmap
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6a37ab8
add --clusterUsingSamples to plotHeatmap and plotProfiler
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db0cec3
add --refPointLabel to plotProfiler and remove conditional
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be71e73
add --labels --addLabels to plotPCA and plotProfile
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d39586f
add --transcriptID --transcript_id_designator to computeMatrixOperations
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3c907ad
Use correct param defaults
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4f0b3e7
remove duplicate use of params in plotEnrichment
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bd65c15
simplify and merge common params into macros
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a520f4a

Commits on Sep 11, 2026

fix cheetah to match param datatypes
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86e5e29
make conditionals and repeats in tests compatible with newer profiles
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122d919

Commits on Sep 12, 2026

Fix most of the tests
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547d678
add additional test outputs
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c513f5d
fix more tests
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84e3893
Fix cheetah error in plotPCA and plotCorrelaton
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2dbbaf7
fix --samplesLabels param in bamPEFragmentSize.xml
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fb882b4
try image_diff
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598d097
replace sim_size with image_diff
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4e9e698
updates images
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f6bb29b