Repository revision
29:d9a637e83828

Repository 'deeptools_compute_matrix'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix

computeMatrix tool metadata
Miscellaneous
prepares data for plotting a heatmap or a profile of given regions
deeptools_compute_matrix
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.2+galaxy0
3.5.2+galaxy0
computeMatrix --version
True
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
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.2+galaxy0 (this tool)
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 3.5.2 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

    
None
False
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