Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.2.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.1.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.7.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.4.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.4.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.6.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.5.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.0.1.0 |
deeptools_compute_matrix |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
deeptools | 3.5.4 | package |
samtools | 1.9 | package |
Additional information about this tool |
#if $custom_sample_labels_conditional.custom_labels_select == "Yes": #set custom_labels=$custom_sample_labels_conditional.labels #end if #set files=[] #set labels=[] #import re #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) ln -f -s '${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($f.bigwigfiles.element_identifier)) ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' && #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #end if #if $custom_sample_labels_conditional.custom_labels_select == "Yes": #set labels=custom_labels #end if #set bed_files=[] #for $counter, $rf, in enumerate($regionsFiles): #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier)) ln -f -s '${rf.regionsFile}' '${identifier}_${counter}.bed' && #silent $bed_files.append('%s_%s.bed' % ($identifier, $counter)) #end for computeMatrix $mode.mode_select --regionsFileName '#echo "' '".join($bed_files)#' --scoreFileName #echo ' '.join($files)# --outFileName '$outFileName' --samplesLabel #echo ' '.join($labels)# --numberOfProcessors "\${GALAXY_SLOTS:-4}" #if $output.showOutputSettings == "yes" #if $output.saveMatrix: --outFileNameMatrix '$outFileNameMatrix' #end if #if $output.saveSortedRegions: --outFileSortedRegions '$outFileSortedRegions' #end if #end if #if $mode.mode_select == "reference-point": --referencePoint $mode.referencePoint $mode.nanAfterEnd --beforeRegionStartLength $mode.beforeRegionStartLength --afterRegionStartLength $mode.afterRegionStartLength #else --regionBodyLength $mode.regionBodyLength #if $mode.regionStartLength.regionStartLength_select == "yes": --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength --unscaled5prime $mode.regionStartLength.unscaled5prime --unscaled3prime $mode.regionStartLength.unscaled3prime #end if #end if #if $advancedOpt.showAdvancedOpt == "yes": --sortRegions '$advancedOpt.sortRegions' --sortUsing '$advancedOpt.sortUsing' --averageTypeBins '$advancedOpt.averageTypeBins' $advancedOpt.skipZeros $advancedOpt.missingDataAsZero --binSize $advancedOpt.binSize #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '': --minThreshold $advancedOpt.minThreshold #end if #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '': --maxThreshold $advancedOpt.maxThreshold #end if #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': --scale $advancedOpt.scale #end if $advancedOpt.metagene #if $advancedOpt.transcriptID: --transcriptID $advancedOpt.transcriptID #end if #if $advancedOpt.exonID: --exonID $advancedOpt.exonID #end if #if $advancedOpt.transcript_id_designator: --transcript_id_designator $advancedOpt.transcript_id_designator #end if #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': #set blfiles=[] #for $f in $advancedOpt.blackListFileName: #silent $blfiles.append("'%s'" % $f) #end for #if $blfiles != ["'None'"]: --blackListFileName #echo ' '.join($blfiles)# #end if #end if #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
regionsFiles_0|regionsFile: computeMatrix1.bed multibigwig_conditional|bigwigfiles: bamCoverage_result4.bw mode|beforeRegionStartLength: 10 mode|afterRegionStartLength: 10 mode|mode_select: reference-point advancedOpt|binSize: 10 advancedOpt|sortUsing: sum advancedOpt|averageTypeBins: sum advancedOpt|showAdvancedOpt: yes |
name: value |
computeMatrix1.bed bamCoverage_result4.bw value |
Test-2 |
regionsFiles_0|regionsFile: computeMatrix2.bed multibigwig_conditional|bigwigfiles: computeMatrix2.bw mode|beforeRegionStartLength: 10 mode|afterRegionStartLength: 10 mode|mode_select: reference-point advancedOpt|binSize: 10 advancedOpt|showAdvancedOpt: yes |
name: value |
computeMatrix2.bed computeMatrix2.bw value |
Test-3 |
regionsFiles_0|regionsFile: computeMatrix2.bed multibigwig_conditional|bigwigfiles: computeMatrix2.bw mode|mode_select: scale-regions advancedOpt|showAdvancedOpt: yes |
name: value |
computeMatrix2.bed computeMatrix2.bw value |