Repository revision
21:c03c3384cd81

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

plotEnrichment tool metadata
Miscellaneous
plots read/fragment coverage over sets of regions
deeptools_plot_enrichment
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.2+galaxy0
3.5.2+galaxy0
plotEnrichment --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.5.0
deeptools_plot_enrichment
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 $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

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

            --plotFile '$outFileName'

            --bamfiles #echo " ".join($files)#
            --labels #echo " ".join($labels)#

            

        #set files=[]
        #set labels=[]
        #for $f in $BED:
            #silent $files.append("'%s'" % $f)
            #silent $labels.append("'%s'" % $f.display_name)
        #end for
        #if len($files) > 0:
            --BED #echo ' '.join($files)#
            --regionLabels #echo ' '.join($labels)#
        #end if

    

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

            --plotFileFormat '$outFileFormat'

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

            #if $advancedOpt.showAdvancedOpt == "yes"
                #if $advancedOpt.attributeKey:
                    --attributeKey '$advancedOpt.attributeKey'
                #end if

                #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
                    --labels $advancedOpt.labels
                #end if

                #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
                    --regionLabels $advancedOpt.regionLabels
                #end if

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if

                $advancedOpt.perSample

                $advancedOpt.variableScales
                
                $advancedOpt.perSample

                $advancedOpt.variableScales

                --plotWidth '$advancedOpt.plotWidth'

                --plotHeight '$advancedOpt.plotHeight'

                #if str($advancedOpt.colors).strip() != "":
                    --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                #end if

                --numPlotsPerRow '$advancedOpt.numPlotsPerRow'

                --alpha '$advancedOpt.alpha'

                
        #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
    

                #if $advancedOpt.Offset:
                    --Offset $advancedOpt.Offset
                #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

    

                $advancedOpt.keepExons

            #end if

    
None
False
Functional tests
name inputs outputs required files
Test-1 multibam_conditional|bamfiles: ['bowtie2 test1.bam', 'bowtie2 test1.bam']
BED: ['multiBamSummary_regions.bed', 'multiBamSummary_regions.bed']
advancedOpt|regionLabels: up down
advancedOpt|minMappingQuality: 0
advancedOpt|showAdvancedOpt: yes
outRawCounts: True
name: value
name: value
bowtie2 test1.bam
multiBamSummary_regions.bed
value