# HG changeset patch # User bgruening # Date 1494799161 14400 # Node ID 801ca6971efce7ab21a7ce48f409b9617e10450f # Parent c224e8aa3f36da11755eb28b53400f5039417040 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28 diff -r c224e8aa3f36 -r 801ca6971efc deepTools_macros.xml --- a/deepTools_macros.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/deepTools_macros.xml Sun May 14 17:59:21 2017 -0400 @@ -1,10 +1,9 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.5.0 + 2.5.1.0 - python deeptools @@ -25,6 +24,21 @@ + + --plotWidth '$advancedOpt.plotWidth' + --plotHeight '$advancedOpt.plotHeight' + + + + + + + + #if $advancedOpt.doExtendCustom.doExtend == 'custom': --extendReads $advancedOpt.doExtendCustom.extendReadsValue @@ -369,46 +383,26 @@ - + - - + - - - - - - - - - - - - - - - - - - + @@ -416,13 +410,13 @@ - + - - + + @@ -467,16 +461,16 @@ #import re #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): - #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) - ln -s "${bigwig}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) + ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) - ln -s "${f.bigwigfiles}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) + ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && + #silent $files.append('%s_%s.bw' % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #end if diff -r c224e8aa3f36 -r 801ca6971efc plotFingerprint.xml --- a/plotFingerprint.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/plotFingerprint.xml Sun May 14 17:59:21 2017 -0400 @@ -24,7 +24,7 @@ #if $output.JSDsample: #if "'{}'".format($output.JSDsample.display_name) in $labels: #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name)) - --JSDsample "./${JSDidx}.bam" + --JSDsample "${JSDidx}.bam" #end if #end if #end if @@ -53,7 +53,7 @@ - + @@ -87,7 +87,7 @@ - diff -r c224e8aa3f36 -r 801ca6971efc repository_dependencies.xml --- a/repository_dependencies.xml Fri Mar 31 17:44:40 2017 -0400 +++ b/repository_dependencies.xml Sun May 14 17:59:21 2017 -0400 @@ -1,4 +1,4 @@ - + diff -r c224e8aa3f36 -r 801ca6971efc test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Fri Mar 31 17:44:40 2017 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Sun May 14 17:59:21 2017 -0400 @@ -1,6 +1,6 @@ -BAM file : 0.bam +Sample label: bowtie2 test1.bam Sample size: 3 Fragment lengths: diff -r c224e8aa3f36 -r 801ca6971efc test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 17:44:40 2017 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Sun May 14 17:59:21 2017 -0400 @@ -1,3 +1,3 @@ Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0 diff -r c224e8aa3f36 -r 801ca6971efc tool_dependencies.xml --- a/tool_dependencies.xml Fri Mar 31 17:44:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - -