From 73069e4c58d83d498066013a15f8ad2d4f34e720 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 8 Sep 2026 09:08:17 +0200 Subject: [PATCH 01/25] Add Docker container requirement for deepTools Updated requirements to include Docker container for deepTools. --- galaxy/wrapper/deepTools_macros.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 4246a18c45..cba1d748ad 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -5,8 +5,7 @@ 23.2 - - samtools + quay.io/biocontainers/deeptools:4.0.0--py312ha170aba_0 @BINARY@ --version From 32f83d1eb9dda1d968ea077a85c40849087f18ed Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 8 Sep 2026 16:43:33 +0200 Subject: [PATCH 02/25] Update deeptools requirement in deepTools_macros.xml Replaced Docker container requirement with package requirement for deeptools. --- galaxy/wrapper/deepTools_macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index cba1d748ad..4cae055a3a 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -5,7 +5,7 @@ 23.2 - quay.io/biocontainers/deeptools:4.0.0--py312ha170aba_0 + deeptools @BINARY@ --version From 59af6efa5c530c73159eb48a2d48b69431e33124 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 9 Sep 2026 23:00:19 +0200 Subject: [PATCH 03/25] testing an obsolete param --- galaxy/wrapper/bamCoverage.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml index 36b6b200cb..ad80dae130 100644 --- a/galaxy/wrapper/bamCoverage.xml +++ b/galaxy/wrapper/bamCoverage.xml @@ -164,6 +164,10 @@ + + + + From e651df576c76a825e7eea563c56ba79aa009361d Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 00:36:49 +0200 Subject: [PATCH 04/25] use *_old binaries --- galaxy/wrapper/alignmentSieve.xml | 2 +- galaxy/wrapper/bamCompare.xml | 2 +- galaxy/wrapper/bamCoverage.xml | 6 +----- galaxy/wrapper/computeMatrix.xml | 2 +- galaxy/wrapper/multiBamSummary.xml | 2 +- 5 files changed, 5 insertions(+), 9 deletions(-) diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml index b6b5ef0d2b..533700653b 100644 --- a/galaxy/wrapper/alignmentSieve.xml +++ b/galaxy/wrapper/alignmentSieve.xml @@ -1,7 +1,7 @@ Filter BAM/CRAM files according to specified parameters - alignmentSieve + alignmentSieve_old deepTools_macros.xml diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index 0e012b5747..cd724e197d 100644 --- a/galaxy/wrapper/bamCompare.xml +++ b/galaxy/wrapper/bamCompare.xml @@ -1,7 +1,7 @@ normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them - bamCompare + bamCompare_old deepTools_macros.xml diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml index ad80dae130..72f541bf0e 100644 --- a/galaxy/wrapper/bamCoverage.xml +++ b/galaxy/wrapper/bamCoverage.xml @@ -1,7 +1,7 @@ generates a coverage bigWig file from a given BAM or CRAM file - bamCoverage + bamCoverage_old deepTools_macros.xml @@ -164,10 +164,6 @@ - - - - diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml index b2f46cf742..3aa8e89050 100644 --- a/galaxy/wrapper/computeMatrix.xml +++ b/galaxy/wrapper/computeMatrix.xml @@ -1,7 +1,7 @@ prepares data for plotting a heatmap or a profile of given regions - computeMatrix + computeMatrix_old deepTools_macros.xml diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml index c198a26020..41303d0f28 100644 --- a/galaxy/wrapper/multiBamSummary.xml +++ b/galaxy/wrapper/multiBamSummary.xml @@ -1,7 +1,7 @@ calculates average read coverages for a list of two or more BAM/CRAM files - multiBamSummary + multiBamSummary_old deepTools_macros.xml From 93704d19ae81bd45dbaff0ae7f85840cf2d5e5ca Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 11:31:49 +0200 Subject: [PATCH 05/25] revert old binary usage --- galaxy/wrapper/alignmentSieve.xml | 2 +- galaxy/wrapper/bamCompare.xml | 2 +- galaxy/wrapper/bamCoverage.xml | 2 +- galaxy/wrapper/computeMatrix.xml | 2 +- galaxy/wrapper/multiBamSummary.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml index 533700653b..b6b5ef0d2b 100644 --- a/galaxy/wrapper/alignmentSieve.xml +++ b/galaxy/wrapper/alignmentSieve.xml @@ -1,7 +1,7 @@ Filter BAM/CRAM files according to specified parameters - alignmentSieve_old + alignmentSieve deepTools_macros.xml diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index cd724e197d..0e012b5747 100644 --- a/galaxy/wrapper/bamCompare.xml +++ b/galaxy/wrapper/bamCompare.xml @@ -1,7 +1,7 @@ normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them - bamCompare_old + bamCompare deepTools_macros.xml diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml index 72f541bf0e..36b6b200cb 100644 --- a/galaxy/wrapper/bamCoverage.xml +++ b/galaxy/wrapper/bamCoverage.xml @@ -1,7 +1,7 @@ generates a coverage bigWig file from a given BAM or CRAM file - bamCoverage_old + bamCoverage deepTools_macros.xml diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml index 3aa8e89050..b2f46cf742 100644 --- a/galaxy/wrapper/computeMatrix.xml +++ b/galaxy/wrapper/computeMatrix.xml @@ -1,7 +1,7 @@ prepares data for plotting a heatmap or a profile of given regions - computeMatrix_old + computeMatrix deepTools_macros.xml diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml index 41303d0f28..c198a26020 100644 --- a/galaxy/wrapper/multiBamSummary.xml +++ b/galaxy/wrapper/multiBamSummary.xml @@ -1,7 +1,7 @@ calculates average read coverages for a list of two or more BAM/CRAM files - multiBamSummary_old + multiBamSummary deepTools_macros.xml From aff01a6bdb097a725d00f32097cc60fe7906f0c7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 11:38:22 +0200 Subject: [PATCH 06/25] remove --ignoreDuplicates from bamCoverage, bamCompare, multiBamSummary, plotCoverage, plotFingerprint and plotEnrichment --- galaxy/wrapper/deepTools_macros.xml | 2 -- galaxy/wrapper/plotFingerprint.xml | 1 - 2 files changed, 3 deletions(-) diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 4cae055a3a..6e228d04cc 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -45,7 +45,6 @@ #else if $advancedOpt.doExtendCustom.doExtend == 'yes': --extendReads #end if - $advancedOpt.ignoreDuplicates $advancedOpt.centerReads #if $advancedOpt.minMappingQuality: --minMappingQuality $advancedOpt.minMappingQuality @@ -211,7 +210,6 @@ - diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml index 436e0c2ac6..d7199e2a0c 100644 --- a/galaxy/wrapper/plotFingerprint.xml +++ b/galaxy/wrapper/plotFingerprint.xml @@ -40,7 +40,6 @@ --binSize '$advancedOpt.binSize' --numberOfSamples '$advancedOpt.numberOfSamples' - $advancedOpt.ignoreDuplicates $advancedOpt.skipZeros #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": From 09c003243377ede66ef4a3e4e80a09aefdaf3002 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 11:43:51 +0200 Subject: [PATCH 07/25] Remove --exactScaling entirely --- galaxy/wrapper/bamCompare.xml | 2 -- galaxy/wrapper/bamCoverage.xml | 2 -- galaxy/wrapper/deepTools_macros.xml | 12 ------------ 3 files changed, 16 deletions(-) diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index 0e012b5747..fe172da798 100644 --- a/galaxy/wrapper/bamCompare.xml +++ b/galaxy/wrapper/bamCompare.xml @@ -46,7 +46,6 @@ #end if --operation $comparison.type - $exactScaling #if $comparison.type in ['ratio','log2']: --pseudocount $comparison.pseudocount @@ -142,7 +141,6 @@ - diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml index 36b6b200cb..50d3063eeb 100644 --- a/galaxy/wrapper/bamCoverage.xml +++ b/galaxy/wrapper/bamCoverage.xml @@ -41,7 +41,6 @@ #if str($region).strip() != '': --region '$region' #end if - $exactScaling #if $advancedOpt.showAdvancedOpt == "yes": #if str($advancedOpt.scaleFactor).strip() != '': @@ -96,7 +95,6 @@ - diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 6e228d04cc..54b0d91bd6 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -667,18 +667,6 @@ is vital to you, select Yes below."> - - - - From 094bf3f089b95fcdccfcc6497216bf3ac038ea29 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 12:54:53 +0200 Subject: [PATCH 08/25] Remove SES option for --scaleFactorsMethod, --sampleLength and --numberOfSamples params --- galaxy/wrapper/bamCompare.xml | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index fe172da798..492df8d72e 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:$scaling.scaleFactor2' @@ -83,17 +79,9 @@ - - - - - From 2e6b71eb0709433a59ad626a4a5e9015825b0e56 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 13:03:54 +0200 Subject: [PATCH 09/25] Remove plotly inputs and outputs everywhere --- galaxy/wrapper/bamPEFragmentSize.xml | 1 - galaxy/wrapper/computeGCBias.xml | 2 -- galaxy/wrapper/deepTools_macros.xml | 5 +---- 3 files changed, 1 insertion(+), 7 deletions(-) diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml index a7eb0d96e4..43a7699ba7 100644 --- a/galaxy/wrapper/bamPEFragmentSize.xml +++ b/galaxy/wrapper/bamPEFragmentSize.xml @@ -90,7 +90,6 @@ - diff --git a/galaxy/wrapper/computeGCBias.xml b/galaxy/wrapper/computeGCBias.xml index e04ca2bbff..6b944bf721 100644 --- a/galaxy/wrapper/computeGCBias.xml +++ b/galaxy/wrapper/computeGCBias.xml @@ -90,7 +90,6 @@ - @@ -105,7 +104,6 @@ - diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 54b0d91bd6..922cb60061 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -691,12 +691,11 @@ is vital to you, select Yes below."> - + - @@ -711,7 +710,6 @@ is vital to you, select Yes below."> - @@ -722,7 +720,6 @@ is vital to you, select Yes below."> - From e48dc0f37894fdfba0561dff701e71542deacd52 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 13:10:28 +0200 Subject: [PATCH 10/25] Remove --plotTitle from bigwigCompare --- galaxy/wrapper/bigwigCompare.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml index 1752842362..b67e8073a6 100644 --- a/galaxy/wrapper/bigwigCompare.xml +++ b/galaxy/wrapper/bigwigCompare.xml @@ -32,9 +32,6 @@ --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' --binSize $advancedOpt.binSize - #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": - --plotTitle '$advancedOpt.plotTitle' - #end if @blacklist@ #end if @@ -98,7 +95,6 @@ - From 2f95e16ea86eb59460a979f4bdc953c556d44ab4 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 13:27:15 +0200 Subject: [PATCH 11/25] add --no_collapse option and include it in tests --- galaxy/wrapper/bamCompare.xml | 4 +++- galaxy/wrapper/bigwigCompare.xml | 7 ++++--- galaxy/wrapper/deepTools_macros.xml | 5 +++++ 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index 492df8d72e..7cc6a645fd 100644 --- a/galaxy/wrapper/bamCompare.xml +++ b/galaxy/wrapper/bamCompare.xml @@ -57,6 +57,7 @@ #end if @ADVANCED_OPTS_READ_PROCESSING@ + $advancedOpt.no_collapse $advancedOpt.skipNAs $advancedOpt.skipZeroOverZero @@ -143,7 +144,7 @@ - + @@ -221,6 +222,7 @@ + diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml index b67e8073a6..4e9129f940 100644 --- a/galaxy/wrapper/bigwigCompare.xml +++ b/galaxy/wrapper/bigwigCompare.xml @@ -26,7 +26,7 @@ #end if #if $advancedOpt.showAdvancedOpt == "yes": - + $advancedOpt.no_collapse $advancedOpt.skipNAs $advancedOpt.skipZeroOverZero --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' @@ -91,7 +91,7 @@ - + @@ -120,8 +120,9 @@ - + + diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 922cb60061..3601119634 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -925,4 +925,9 @@ is vital to you, select Yes below."> + + + From d3ade57d3af167381c04b37b6d3dcc8a4ee09b90 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 13:39:24 +0200 Subject: [PATCH 12/25] add --sortUsingSamples to computeMatrix --- galaxy/wrapper/computeMatrix.xml | 4 ++++ galaxy/wrapper/deepTools_macros.xml | 13 +++++++++++++ galaxy/wrapper/plotHeatmap.xml | 15 +++------------ 3 files changed, 20 insertions(+), 12 deletions(-) diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml index b2f46cf742..cfee272349 100644 --- a/galaxy/wrapper/computeMatrix.xml +++ b/galaxy/wrapper/computeMatrix.xml @@ -59,6 +59,9 @@ #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 @@ -169,6 +172,7 @@ + region length + + + + + + + + + + - - - - - - - + Date: Thu, 10 Sep 2026 15:35:31 +0200 Subject: [PATCH 13/25] add --chromosomesToSkip and a test to multiBigwigSummary --- galaxy/wrapper/multiBigwigSummary.xml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/galaxy/wrapper/multiBigwigSummary.xml index b63db25d58..6f24164601 100644 --- a/galaxy/wrapper/multiBigwigSummary.xml +++ b/galaxy/wrapper/multiBigwigSummary.xml @@ -34,6 +34,10 @@ --BED $mode.region_file #end if + #if $chromosomesToSkip.strip() != '': + --chromosomesToSkip '$chromosomesToSkip' + #end if + #if str($region.value) != '': --region '$region' #end if @@ -71,6 +75,9 @@ + @@ -90,6 +97,7 @@ + @@ -104,6 +112,19 @@ + + + + + + + + + + + + + Date: Thu, 10 Sep 2026 15:49:17 +0200 Subject: [PATCH 14/25] add --fixedStep param and a test to bigwigCompare --- galaxy/wrapper/bigwigCompare.xml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml index 4e9129f940..5661429916 100644 --- a/galaxy/wrapper/bigwigCompare.xml +++ b/galaxy/wrapper/bigwigCompare.xml @@ -94,6 +94,8 @@ + @@ -127,6 +129,17 @@ + + + + + + + + + + + Date: Thu, 10 Sep 2026 15:57:11 +0200 Subject: [PATCH 15/25] add --boxAroundHeatmaps param and a test to plotHeatmap --- galaxy/wrapper/plotHeatmap.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index 82cf30aac0..c3a798653e 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -91,6 +91,7 @@ --heatmapWidth $advancedOpt.heatmapWidth --heatmapHeight $advancedOpt.heatmapHeight + --boxAroundHeatmaps $advancedOpt.boxAroundHeatmaps --whatToShow '$advancedOpt.whatToShow' --startLabel '$advancedOpt.startLabel' @@ -195,6 +196,9 @@ + + @@ -261,6 +265,7 @@ + From 12756f958085a6626e7df182d14896087e7ab4f5 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 15:58:17 +0200 Subject: [PATCH 16/25] add fixedStep commandline --- galaxy/wrapper/bigwigCompare.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml index 5661429916..61d4689b29 100644 --- a/galaxy/wrapper/bigwigCompare.xml +++ b/galaxy/wrapper/bigwigCompare.xml @@ -28,6 +28,7 @@ #if $advancedOpt.showAdvancedOpt == "yes": $advancedOpt.no_collapse $advancedOpt.skipNAs + $advancedOpt.fixedStep $advancedOpt.skipZeroOverZero --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' --binSize $advancedOpt.binSize From 6924c720d1fb32511d3973dfb055b6c9e83ed053 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 16:24:40 +0200 Subject: [PATCH 17/25] add --ggplot param --- galaxy/wrapper/bamPEFragmentSize.xml | 2 ++ galaxy/wrapper/deepTools_macros.xml | 6 ++++++ galaxy/wrapper/plotCorrelation.xml | 3 ++- galaxy/wrapper/plotCoverage.xml | 2 ++ galaxy/wrapper/plotEnrichment.xml | 4 ++++ galaxy/wrapper/plotFingerprint.xml | 2 ++ galaxy/wrapper/plotHeatmap.xml | 2 ++ galaxy/wrapper/plotPCA.xml | 2 ++ galaxy/wrapper/plotProfiler.xml | 2 ++ 9 files changed, 24 insertions(+), 1 deletion(-) diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml index 43a7699ba7..bc8df7aaac 100644 --- a/galaxy/wrapper/bamPEFragmentSize.xml +++ b/galaxy/wrapper/bamPEFragmentSize.xml @@ -33,6 +33,7 @@ #if $advancedOpt.outRawFragmentLengths --outRawFragmentLengths '$fragLengths' #end if + $advancedOpt.ggplot #end if > '$outfile' ]]> @@ -78,6 +79,7 @@ label="Maximum fragment length" help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length"/> + diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 7440daf185..a45c7b7053 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -379,6 +379,12 @@ + + + + + .. class:: infomark diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml index f15c8b819c..79af4343ea 100644 --- a/galaxy/wrapper/plotCorrelation.xml +++ b/galaxy/wrapper/plotCorrelation.xml @@ -32,7 +32,7 @@ #if $outFileCorMatrix: --outFileCorMatrix '$matrix' #end if - + $ggplot ]]> @@ -100,6 +100,7 @@ unusually high counts."/> + diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml index ee925b9a16..247423ca96 100644 --- a/galaxy/wrapper/plotCoverage.xml +++ b/galaxy/wrapper/plotCoverage.xml @@ -54,6 +54,7 @@ #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if + $advancedOpt.ggplot @ADVANCED_OPTS_READ_PROCESSING@ @PLOTWIDTHHEIGHT@ @blacklist@ @@ -99,6 +100,7 @@ + diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml index 265d150e5e..95c9b4a5f9 100644 --- a/galaxy/wrapper/plotEnrichment.xml +++ b/galaxy/wrapper/plotEnrichment.xml @@ -65,6 +65,8 @@ --alpha '$advancedOpt.alpha' + $advancedOpt.ggplot + @ADVANCED_OPTS_READ_PROCESSING@ #if $advancedOpt.Offset: @@ -141,6 +143,8 @@ label="Number of plots/row" help="" /> + + + diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index c3a798653e..3bbb92ed15 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -116,6 +116,7 @@ --labelRotation '$advancedOpt.labelRotation' $advancedOpt.perGroup + $advancedOpt.ggplot @KMEANS_CLUSTERING@ @@ -238,6 +239,7 @@ label="Make one plot per group of regions" help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/> + + diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml index ff7d7d07b0..c63b08cd93 100644 --- a/galaxy/wrapper/plotProfiler.xml +++ b/galaxy/wrapper/plotProfiler.xml @@ -72,6 +72,7 @@ --outFileNameData '$output_outFileNameData' #end if + $advancedOpt.ggplot @KMEANS_CLUSTERING@ #end if @@ -179,6 +180,7 @@ + From 6a37ab8bff61380f648dbd888ebdbd0bd22be14e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 16:40:32 +0200 Subject: [PATCH 18/25] add --interpolationMethod to plotHeatmap --- galaxy/wrapper/plotHeatmap.xml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index 3bbb92ed15..e7a9bc1b82 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -28,6 +28,7 @@ #else --plotFileFormat 'png' #end if + --interpolationMethod '$interpolationMethod' #if $advancedOpt.showAdvancedOpt == "yes" #if $advancedOpt.sortRegions: @@ -132,7 +133,14 @@ - + + + + + + + @@ -262,6 +270,7 @@ + From db0cec38ac3cbf8daf64f65349798bc8ce5f5ddc Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 17:03:37 +0200 Subject: [PATCH 19/25] add --clusterUsingSamples to plotHeatmap and plotProfiler --- galaxy/wrapper/deepTools_macros.xml | 12 ++++++++++++ galaxy/wrapper/plotHeatmap.xml | 11 +---------- galaxy/wrapper/plotProfiler.xml | 8 ++++++++ 3 files changed, 21 insertions(+), 10 deletions(-) diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index a45c7b7053..1953e9a62b 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -129,6 +129,18 @@ 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."/> + + + + + + + + + diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index e7a9bc1b82..133718bed7 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -249,16 +249,7 @@ - - - - - - - + diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml index c63b08cd93..aa99c866df 100644 --- a/galaxy/wrapper/plotProfiler.xml +++ b/galaxy/wrapper/plotProfiler.xml @@ -55,6 +55,7 @@ --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# #end if + --numPlotsPerRow $advancedOpt.numPlotsPerRow --legendLocation '$advancedOpt.legendLocation' --labelRotation '$advancedOpt.labelRotation' @@ -72,6 +73,10 @@ --outFileNameData '$output_outFileNameData' #end if + #if str($advancedOpt.clusterUsingSamples).strip() != "": + --clusterUsingSamples '$advancedOpt.clusterUsingSamples' + #end if + $advancedOpt.ggplot @KMEANS_CLUSTERING@ @@ -165,6 +170,8 @@ all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value) + @@ -182,6 +189,7 @@ + From be71e73867af71cbf99ba17827104e640abc116a Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 17:48:00 +0200 Subject: [PATCH 20/25] add --refPointLabel to plotProfiler and remove conditional --- galaxy/wrapper/plotHeatmap.xml | 7 +++-- galaxy/wrapper/plotProfiler.xml | 49 ++++++++++++++++----------------- 2 files changed, 27 insertions(+), 29 deletions(-) diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index 133718bed7..4cb212e110 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -98,7 +98,9 @@ --startLabel '$advancedOpt.startLabel' --endLabel '$advancedOpt.endLabel' - --refPointLabel '$advancedOpt.referencePointLabel' + #if str($advancedOpt.refPointLabel).strip() != "": + --refPointLabel '$advancedOpt.refPointLabel' + #end if #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "": --samplesLabel $advancedOpt.samplesLabel @@ -221,8 +223,7 @@ - - - - - - - - - - - - - + + + @@ -204,17 +199,19 @@ - - - - - + + + + + + + + - From d39586fc545307ca919fcb2bdc702b1833e216aa Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 18:07:09 +0200 Subject: [PATCH 21/25] add --labels --addLabels to plotPCA and plotProfile --- galaxy/wrapper/deepTools_macros.xml | 38 ++++++++++++++--------------- galaxy/wrapper/plotCorrelation.xml | 3 ++- galaxy/wrapper/plotPCA.xml | 6 +++++ 3 files changed, 27 insertions(+), 20 deletions(-) diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 1953e9a62b..87562c5f96 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -461,25 +461,25 @@ is vital to you, select Yes below."> - - - - - - - - - - - - - - - - [A-Za-z0-9 =-_/+]+ - - - + + + + + + + + + + + + + + + + [A-Za-z0-9 =-_/+]+ + + + diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml index 79af4343ea..26330168aa 100644 --- a/galaxy/wrapper/plotCorrelation.xml +++ b/galaxy/wrapper/plotCorrelation.xml @@ -11,6 +11,7 @@ --corData '$corData' --plotFile '$outFileName' --corMethod '$corMethod' + --labels #echo " ".join($labels) --whatToPlot '$plotting_type.whatToPlot' #if str($plotting_type.whatToPlot) == 'heatmap': @HEATMAP_OPTIONS@ @@ -38,7 +39,7 @@ - + diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml index 5fd43efecf..9f52f3edd4 100644 --- a/galaxy/wrapper/plotPCA.xml +++ b/galaxy/wrapper/plotPCA.xml @@ -10,6 +10,7 @@ @BINARY@ --corData '$corData' --plotTitle '$plotTitle' + --labels #echo " ".join($labels) --plotFile '$outFileName' --plotFileFormat '$outFileFormat' #if str($advancedOpt.showAdvancedOpt) == 'yes': @@ -25,6 +26,7 @@ #if $advancedOpt.markers: --markers $advancedOpt.markers #end if + $advancedOpt.addLabels $advancedOpt.ggplot #end if #if $outFileNameData @@ -36,6 +38,7 @@ + @@ -56,6 +59,9 @@ 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." /> + From 3c907adc3902d72a91ad38166014486e91696e1f Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 18:18:25 +0200 Subject: [PATCH 22/25] add --transcriptID --transcript_id_designator to computeMatrixOperations --- galaxy/wrapper/computeMatrixOperations.xml | 15 +++++++++++++++ galaxy/wrapper/correctGCBias.xml | 7 +++++++ 2 files changed, 22 insertions(+) diff --git a/galaxy/wrapper/computeMatrixOperations.xml b/galaxy/wrapper/computeMatrixOperations.xml index d0b477b669..472e682a51 100755 --- a/galaxy/wrapper/computeMatrixOperations.xml +++ b/galaxy/wrapper/computeMatrixOperations.xml @@ -70,6 +70,12 @@ #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 -o $outFileName #else if $submodule.command == "dataRange": dataRange @@ -147,6 +153,15 @@ + + diff --git a/galaxy/wrapper/correctGCBias.xml b/galaxy/wrapper/correctGCBias.xml index b2293aaf34..d8aca4eafb 100644 --- a/galaxy/wrapper/correctGCBias.xml +++ b/galaxy/wrapper/correctGCBias.xml @@ -30,6 +30,7 @@ #if str($region).strip() != '': --region '$region' #end if + --binSize $binSize --correctedFile corrected.bam ]]> @@ -40,6 +41,12 @@ + + From 4f0b3e753887e7b23c99ed836b5aba712efa3ce0 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 18:44:13 +0200 Subject: [PATCH 23/25] Use correct param defaults --- galaxy/wrapper/computeMatrix.xml | 12 ++++++------ galaxy/wrapper/plotCoverage.xml | 2 +- galaxy/wrapper/plotFingerprint.xml | 2 +- galaxy/wrapper/plotPCA.xml | 2 +- galaxy/wrapper/plotProfiler.xml | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml index cfee272349..a61657087e 100644 --- a/galaxy/wrapper/computeMatrix.xml +++ b/galaxy/wrapper/computeMatrix.xml @@ -108,7 +108,7 @@ - @@ -117,11 +117,11 @@ - - @@ -146,10 +146,10 @@ 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)"/> - - @@ -166,7 +166,7 @@ - diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml index 247423ca96..2eccc7d451 100644 --- a/galaxy/wrapper/plotCoverage.xml +++ b/galaxy/wrapper/plotCoverage.xml @@ -91,7 +91,7 @@ - diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml index 4992a9be3c..1e186374c1 100644 --- a/galaxy/wrapper/plotFingerprint.xml +++ b/galaxy/wrapper/plotFingerprint.xml @@ -67,7 +67,7 @@ - diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml index 9f52f3edd4..0ab260d6b3 100644 --- a/galaxy/wrapper/plotPCA.xml +++ b/galaxy/wrapper/plotPCA.xml @@ -47,7 +47,7 @@ - + sum - From bd65c1543292cdc4507a2c5acbdfc51eaeaced69 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 10 Sep 2026 18:47:11 +0200 Subject: [PATCH 24/25] remove duplicate use of params in plotEnrichment --- galaxy/wrapper/plotEnrichment.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml index 95c9b4a5f9..cabed18271 100644 --- a/galaxy/wrapper/plotEnrichment.xml +++ b/galaxy/wrapper/plotEnrichment.xml @@ -49,10 +49,6 @@ $advancedOpt.variableScales - $advancedOpt.perSample - - $advancedOpt.variableScales - --plotWidth '$advancedOpt.plotWidth' --plotHeight '$advancedOpt.plotHeight' From a520f4aa939da525ff862247f23c507b680b6a0c Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 11 Sep 2026 01:57:54 +0200 Subject: [PATCH 25/25] simplify and merge common params into macros --- galaxy/wrapper/bamCompare.xml | 35 +-- galaxy/wrapper/bamCoverage.xml | 87 +++--- galaxy/wrapper/bamPEFragmentSize.xml | 47 ++- galaxy/wrapper/bigwigAverage.xml | 23 +- galaxy/wrapper/bigwigCompare.xml | 31 +- galaxy/wrapper/computeGCBias.xml | 37 +-- galaxy/wrapper/computeMatrix.xml | 103 +++---- galaxy/wrapper/computeMatrixOperations.xml | 18 +- galaxy/wrapper/deepTools_macros.xml | 321 ++++++++++++++------- galaxy/wrapper/estimateReadFiltering.xml | 5 +- galaxy/wrapper/multiBamSummary.xml | 76 +---- galaxy/wrapper/multiBigwigSummary.xml | 74 +---- galaxy/wrapper/plotCoverage.xml | 33 +-- galaxy/wrapper/plotEnrichment.xml | 15 +- galaxy/wrapper/plotFingerprint.xml | 36 +-- galaxy/wrapper/plotHeatmap.xml | 215 +++++--------- galaxy/wrapper/plotPCA.xml | 43 ++- galaxy/wrapper/plotProfiler.xml | 174 +++-------- 18 files changed, 575 insertions(+), 798 deletions(-) diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml index 7cc6a645fd..39d0630b38 100644 --- a/galaxy/wrapper/bamCompare.xml +++ b/galaxy/wrapper/bamCompare.xml @@ -135,28 +135,21 @@ - - - - - - - - - - - - + + + + + + - - - - + + + diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml index 50d3063eeb..1f820d5be3 100644 --- a/galaxy/wrapper/bamCoverage.xml +++ b/galaxy/wrapper/bamCoverage.xml @@ -97,55 +97,48 @@ - - + + + + + + + + + + + + + + - + + - - - - - - - - - - - - - - - - - - - - - - + + diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml index bc8df7aaac..120dc99d6d 100644 --- a/galaxy/wrapper/bamPEFragmentSize.xml +++ b/galaxy/wrapper/bamPEFragmentSize.xml @@ -54,34 +54,25 @@ - - - - - - - - - - - - - - - - - + + + + + + + + + + diff --git a/galaxy/wrapper/bigwigAverage.xml b/galaxy/wrapper/bigwigAverage.xml index 79e613d5c4..18c32bfbc9 100644 --- a/galaxy/wrapper/bigwigAverage.xml +++ b/galaxy/wrapper/bigwigAverage.xml @@ -38,22 +38,15 @@ - - - - - - - - + + - - - - - + + + + diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml index 61d4689b29..d60bad7f1d 100644 --- a/galaxy/wrapper/bigwigCompare.xml +++ b/galaxy/wrapper/bigwigCompare.xml @@ -82,25 +82,18 @@ - - - - - - - - - - - - - - - - + + + + + + + + + diff --git a/galaxy/wrapper/computeGCBias.xml b/galaxy/wrapper/computeGCBias.xml index 6b944bf721..04779c04cb 100644 --- a/galaxy/wrapper/computeGCBias.xml +++ b/galaxy/wrapper/computeGCBias.xml @@ -60,28 +60,21 @@ - - - - - - - - - - - - - + + + + + + diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml index a61657087e..020720a709 100644 --- a/galaxy/wrapper/computeMatrix.xml +++ b/galaxy/wrapper/computeMatrix.xml @@ -159,63 +159,56 @@ - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + diff --git a/galaxy/wrapper/computeMatrixOperations.xml b/galaxy/wrapper/computeMatrixOperations.xml index 472e682a51..62e142e60c 100755 --- a/galaxy/wrapper/computeMatrixOperations.xml +++ b/galaxy/wrapper/computeMatrixOperations.xml @@ -98,11 +98,11 @@ - + - + - + - + @@ -128,7 +128,7 @@ - + - + - + - + @@ -165,7 +165,7 @@ - + diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 87562c5f96..bae3851ef6 100755 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -110,7 +110,7 @@ - @@ -129,79 +129,6 @@ 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."/> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #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 - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $mode.modeOpt + + --outFileName '$outFile' + #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 $region: + --region '$region' + #end if + + .. class:: infomark @@ -488,29 +475,6 @@ is vital to you, select Yes below."> help="Title of the plot, to be printed on top of the generated image."/> - - - - - - - - - - - - - - - - - - - - - + + + + @@ -961,4 +929,159 @@ is vital to you, select Yes below."> label="Adjacent bins that have the same value are collapsed" help="This reduces the size of the output file (drastically)"/> + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/galaxy/wrapper/estimateReadFiltering.xml b/galaxy/wrapper/estimateReadFiltering.xml index 925e8d0368..dab098b561 100644 --- a/galaxy/wrapper/estimateReadFiltering.xml +++ b/galaxy/wrapper/estimateReadFiltering.xml @@ -51,10 +51,7 @@ - - + diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml index c198a26020..2c451cfcb6 100644 --- a/galaxy/wrapper/multiBamSummary.xml +++ b/galaxy/wrapper/multiBamSummary.xml @@ -12,78 +12,32 @@ @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 $advancedOpt.showAdvancedOpt == "yes": - @ADVANCED_OPTS_READ_PROCESSING@ - @ADVANCED_OPTS_GTF@ - @blacklist@ - #end if + @THREADS@ + --bamfiles #echo ' '.join($files)# + + @MULTISUMMARY_COMMON_PARAMS@ + + #if $scalingFactors: + --scalingFactors '$scalingFactorsFile' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + @ADVANCED_OPTS_READ_PROCESSING@ + @ADVANCED_OPTS_GTF@ + @blacklist@ + #end if ]]> - - - - - - - - - - - - - - - - - - - - + - diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/galaxy/wrapper/multiBigwigSummary.xml index 6f24164601..40f4b84004 100644 --- a/galaxy/wrapper/multiBigwigSummary.xml +++ b/galaxy/wrapper/multiBigwigSummary.xml @@ -12,73 +12,27 @@ @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 $chromosomesToSkip.strip() != '': - --chromosomesToSkip '$chromosomesToSkip' - #end if - - #if str($region.value) != '': - --region '$region' - #end if - - #if $advancedOpt.showAdvancedOpt == "yes": - @ADVANCED_OPTS_GTF@ - @blacklist@ - #end if + @THREADS@ + --bwfiles #echo ' '.join($files)# + + @MULTISUMMARY_COMMON_PARAMS@ + + #if $chromosomesToSkip.strip() != '': + --chromosomesToSkip '$chromosomesToSkip' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + @ADVANCED_OPTS_GTF@ + @blacklist@ + #end if ]]> - - - - - - - - - - - - - - - - - + - diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml index 2eccc7d451..e2f53733df 100644 --- a/galaxy/wrapper/plotCoverage.xml +++ b/galaxy/wrapper/plotCoverage.xml @@ -84,27 +84,20 @@ - - - - - - - - - - - - - - - - - + + + + + + + + + + - + diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml index cabed18271..a43641926a 100644 --- a/galaxy/wrapper/plotEnrichment.xml +++ b/galaxy/wrapper/plotEnrichment.xml @@ -49,9 +49,7 @@ $advancedOpt.variableScales - --plotWidth '$advancedOpt.plotWidth' - - --plotHeight '$advancedOpt.plotHeight' + @PLOTWIDTHHEIGHT@ #if str($advancedOpt.colors).strip() != "": --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# @@ -91,13 +89,7 @@ attribute key. For example, the gene_biotype. Note that 'None' is used for BED files or entries where the attributeKey is not found." /> - - - + - - + diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml index 1e186374c1..486d5a4307 100644 --- a/galaxy/wrapper/plotFingerprint.xml +++ b/galaxy/wrapper/plotFingerprint.xml @@ -57,26 +57,19 @@ - - - - - - - - - - - - - - - - + + + + + + + + + @@ -86,6 +79,7 @@ + @@ -101,7 +95,7 @@ (( output['showOutputSettings'] == 'yes' and - output['saveRawCounts'] is True + output['outRawCounts'] is True )) diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml index 4cb212e110..1fac566f5a 100644 --- a/galaxy/wrapper/plotHeatmap.xml +++ b/galaxy/wrapper/plotHeatmap.xml @@ -73,18 +73,9 @@ --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 '$advancedOpt.clusterUsingSamples' - #end if --xAxisLabel '$advancedOpt.xAxisLabel' --yAxisLabel '$advancedOpt.yAxisLabel' @@ -95,40 +86,12 @@ --boxAroundHeatmaps $advancedOpt.boxAroundHeatmaps --whatToShow '$advancedOpt.whatToShow' - --startLabel '$advancedOpt.startLabel' - --endLabel '$advancedOpt.endLabel' - - #if str($advancedOpt.refPointLabel).strip() != "": - --refPointLabel '$advancedOpt.refPointLabel' - #end if - - #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 - $advancedOpt.ggplot - - @KMEANS_CLUSTERING@ - + @HEATMAP_PROFILER_PARAMS@ #end if ]]> - + @@ -143,116 +106,72 @@ - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml index 0ab260d6b3..b7ef53a613 100644 --- a/galaxy/wrapper/plotPCA.xml +++ b/galaxy/wrapper/plotPCA.xml @@ -40,31 +40,24 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml index 6e4232ea06..505231861d 100644 --- a/galaxy/wrapper/plotProfiler.xml +++ b/galaxy/wrapper/plotProfiler.xml @@ -27,167 +27,77 @@ --plotFileFormat 'png' #end if - --startLabel '$startLabel' - --endLabel '$endLabel' - #if str($refPointLabel).strip() != "": - --refPointLabel '$refPointLabel' - #end if - #if $advancedOpt.showAdvancedOpt == "yes": #if $advancedOpt.averageType: --averageType '$advancedOpt.averageType' #end if - --plotHeight $advancedOpt.plotHeight - --plotWidth $advancedOpt.plotWidth + @PLOTWIDTHHEIGHT@ --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 '$advancedOpt.plotTitle' - #end if #if str($advancedOpt.colors).strip() != "": --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# #end if --numPlotsPerRow $advancedOpt.numPlotsPerRow - --legendLocation '$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 #if $advancedOpt.outFileNameData: --outFileNameData '$output_outFileNameData' #end if - #if str($advancedOpt.clusterUsingSamples).strip() != "": - --clusterUsingSamples '$advancedOpt.clusterUsingSamples' - #end if - - $advancedOpt.ggplot - @KMEANS_CLUSTERING@ + @HEATMAP_PROFILER_PARAMS@ #end if ]]> - - - - + - - - - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value) - - - - - - - - - - - - - - - + + + + + + + + + + + + all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value) + + - - + +