Repository revision
28:9368fbc49c8b

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

plotCoverage tool metadata
Miscellaneous
plotCoverage
assesses the sequencing depth of BAM/CRAM files
deeptools_plot_coverage
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.2+galaxy0
3.5.2+galaxy0
plotCoverage --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.0.1.0
deeptools_plot_coverage
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 $multibam_conditional.orderMatters == "No":
            #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                ln -s '${bamfile}' './${counter}.bam' &&
                #if $bamfile.ext == 'bam':
                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                ln -s '${f.bamfiles}' './${counter}.bam' &&
                #if $f.bamfiles.ext == 'bam':
                    ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $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

    

        plotCoverage

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

            --plotFile '$outFileName'
            --bamfiles #echo " ".join($files)#
            --labels #echo " ".join($labels)#
            --plotFileFormat '$outFileFormat'

            #if $outRawCounts:
                --outRawCounts '$outFileRawCounts'
            #end if

            #if ' '.join(map(str, $BED)) != 'None':
                #set bedFileList=[]
                #for $f in $BED:
                    #silent $bedFileList.append("'%s'" % $f)
                #end for
                #if $bedFileList != ["'None'"]:
                    --BED #echo ' '.join($bedFileList)#
                #end if
            #end if

            #if $coverageOpt.showCoverageOpt == "yes":
                --outCoverageMetrics '$outFileCoverageMetrics'
                #for $t in $coverageOpt.thresholds:
                    -ct $t.coverageThreshold
                #end for
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                --numberOfSamples '$advancedOpt.numberOfSamples'
                $advancedOpt.skipZeros

                #if str($advancedOpt.region).strip() != '':
                    --region '$advancedOpt.region'
                #end if
                --numberOfSamples $advancedOpt.numberOfSamples

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if
                
        #if $advancedOpt.doExtendCustom.doExtend == 'custom':
            --extendReads $advancedOpt.doExtendCustom.extendReadsValue
        #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
            --extendReads
        #end if
        $advancedOpt.ignoreDuplicates
        $advancedOpt.centerReads
        #if $advancedOpt.minMappingQuality:
            --minMappingQuality '$advancedOpt.minMappingQuality'
        #end if
        #if $advancedOpt.samFlagInclude:
            --samFlagInclude $advancedOpt.samFlagInclude
        #end if
        #if $advancedOpt.samFlagExclude:
            --samFlagExclude $advancedOpt.samFlagExclude
        #end if
        #if $advancedOpt.minFragmentLength:
            --minFragmentLength $advancedOpt.minFragmentLength
        #end if
        #if $advancedOpt.maxFragmentLength:
            --maxFragmentLength $advancedOpt.maxFragmentLength
        #end if
    
                
        --plotWidth '$advancedOpt.plotWidth'
        --plotHeight '$advancedOpt.plotHeight'
    
                

        #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 multibam_conditional|bamfiles: ['bowtie2 test1.bam', 'bowtie2 test1.bam']
advancedOpt|plotTitle: Test Title from Galaxy
advancedOpt|showAdvancedOpt: yes
outRawCounts: True
name: value
name: value
bowtie2 test1.bam
value
Test-2 multibam_conditional|bamfiles: ['bowtie2 test1.bam', 'bowtie2 test1.bam']
coverageOpt|thresholds_0|coverageThreshold: 20
coverageOpt|thresholds_1|coverageThreshold: 10
coverageOpt|thresholds_2|coverageThreshold: 5
coverageOpt|thresholds_3|coverageThreshold: 0
coverageOpt|showCoverageOpt: yes
advancedOpt|plotTitle: Test Title from Galaxy
advancedOpt|showAdvancedOpt: yes
name: value
name: value
bowtie2 test1.bam
value