Repository revision
29:2d2cf5c1ea8a

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

bamCoverage tool metadata
Miscellaneous
bamCoverage
generates a coverage bigWig file from a given BAM or CRAM file
deeptools_bam_coverage
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.2+galaxy0
3.5.2+galaxy0
bamCoverage --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.0.1.0
deeptools_bam_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
ln -s '$bamInput' one.bam &&
        #if $bamInput.ext == 'bam':
            ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
        #else:
            ln -s '${bamInput.metadata.cram_index}' one.bam.crai &&
        #end if

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

            --bam one.bam
            --outFileName '$outFileName'
            --outFileFormat '$outFileFormat'

            --binSize $binSize

            #if $scaling.type=='rpkm':
                --normalizeUsing RPKM
            #elif $scaling.type=='cpm':
                --normalizeUsing CPM
            #elif $scaling.type=='bpm':
                --normalizeUsing BPM
            #elif $scaling.type=='1x':
                --normalizeUsing RPGC
                #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                    --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize
                #else:
                    --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
                #end if
            #end if

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

            #if $advancedOpt.showAdvancedOpt == "yes":
                #if str($advancedOpt.scaleFactor).strip() != '':
                    --scaleFactor $advancedOpt.scaleFactor
                #end if

                #if $advancedOpt.smoothLength:
                    --smoothLength '$advancedOpt.smoothLength'
                #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
    
                $advancedOpt.skipNAs

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

                #if str($advancedOpt.filterRNAstrand) != 'no':
                    --filterRNAstrand '$advancedOpt.filterRNAstrand'
                #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

    
            #end if

    
None
False
Functional tests
name inputs outputs required files
Test-1 bamInput: bowtie2 test1.bam
binSize: 10
scaling|type: no
outFileFormat: bigwig
advancedOpt|showAdvancedOpt: no
name: value
bowtie2 test1.bam
value
Test-2 bamInput: bowtie2 test1.bam
binSize: 10
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000
scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific
outFileFormat: bigwig
advancedOpt|showAdvancedOpt: no
name: value
bowtie2 test1.bam
value
Test-3 bamInput: bowtie2 test1.bam
binSize: 10
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000
scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific
outFileFormat: bedgraph
advancedOpt|showAdvancedOpt: no
name: value
bowtie2 test1.bam
value
Test-4 bamInput: phiX.bam
binSize: 10
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000
scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific
outFileFormat: bigwig
advancedOpt|showAdvancedOpt: no
name: value
phiX.bam
value
Test-5 bamInput: phiX.bam
binSize: 10
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000
scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific
outFileFormat: bedgraph
advancedOpt|showAdvancedOpt: yes
name: value
phiX.bam
value
Test-6 bamInput: phiX.bam
binSize: 10
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000
scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific
outFileFormat: bigwig
advancedOpt|filterRNAstrand: reverse
advancedOpt|showAdvancedOpt: yes
name: value
phiX.bam
value
Test-7 bamInput: bowtie2 test1.bam
binSize: 10
scaling|type: no
outFileFormat: bigwig
advancedOpt|doExtendCustom|doExtend: yes
advancedOpt|minMappingQuality: 0
advancedOpt|Offset: -4 -1
advancedOpt|showAdvancedOpt: yes
name: value
bowtie2 test1.bam
value