Repository revision
29:195e98217334

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

bamPEFragmentSize tool metadata
Miscellaneous
Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files
deeptools_bam_pe_fragmentsize
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.2+galaxy0
3.5.2+galaxy0
bamPEFragmentSize --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.0.1.0
deeptools_bam_pe_fragmentsize
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

    
        bamPEFragmentSize
            --numberOfProcessors "\${GALAXY_SLOTS:-4}"
            --bamfiles #echo " ".join($files)
            #if $samplesLabel:
                --samplesLabel #echo " ".join($samplesLabel)
            #else:
                --samplesLabel #echo " ".join($labels)
            #end if
            #if $histogram:
                --histogram '$histogram_outfile'
                --plotFileFormat '$outFileFormat'
            #end if
            --plotTitle '$plotTitle'
            #if $advancedOpt.showAdvancedOpt == 'yes'
                --binSize '$advancedOpt.binSize'
                --distanceBetweenBins '$advancedOpt.distanceBetweenBins'
                $advancedOpt.logScale
                --maxFragmentLength '$advancedOpt.maxFragmentLength'
                

        #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

    
                #if $advancedOpt.table
                    --table '$table'
                #end if
                #if $advancedOpt.outRawFragmentLengths
                    --outRawFragmentLengths '$fragLengths'
                #end if
            #end if
            > '$outfile'

    
None
False
Functional tests
name inputs outputs required files
Test-1 multibam_conditional|bamfiles: bowtie2 test1.bam
histogram: True
plotTitle: Test Plot
name: value
name: value
bowtie2 test1.bam
value
Test-2 multibam_conditional|bamfiles: bowtie2 test1.bam
advancedOpt|table: True
advancedOpt|outRawFragmentLengths: True
advancedOpt|showAdvancedOpt: yes
name: value
name: value
bowtie2 test1.bam
value