Repository revision
29:d9ce4897dbb2

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

multiBigwigSummary tool metadata
Miscellaneous
calculates average scores for a list of two or more bigwig files
deeptools_multi_bigwig_summary
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.2+galaxy0
3.5.2+galaxy0
multiBigwigSummary --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.1.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.0.1.0
deeptools_multi_bigwig_summary
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
#set files=[]
        #set labels=[]

        

        #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

    
        multiBigwigSummary
            $mode.modeOpt

            --numberOfProcessors "\${GALAXY_SLOTS:-4}"

            --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 str($region.value) != '':
                --region '$region'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                
        $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 multibigwig_conditional|bigwigfiles: ['test.bw', 'test.bw']
mode|binSize: 10
mode|modeOpt: bins
name: value
test.bw
value
Test-2 multibigwig_conditional|bigwigfiles: ['test.bw', 'test.bw']
custom_sample_labels_conditional|labels: sample1 sample2
custom_sample_labels_conditional|custom_labels_select: Yes
mode|binSize: 10
mode|modeOpt: bins
outRawCounts: True
name: value
name: value
test.bw
value