Repository revision
29:29451af70c52

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

bamCompare tool metadata
Miscellaneous
bamCompare
normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them
deeptools_bam_compare
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.2+galaxy0
3.5.2+galaxy0
bamCompare --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.0.1.0
deeptools_bam_compare
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 '$bamFile1' one.bam &&
        #if $bamFile1.ext == 'bam':
            ln -s '${bamFile1.metadata.bam_index}' one.bam.bai &&
        #else:
            ln -s '${bamFile1.metadata.cram_index}' one.bam.crai &&
        #end if
        ln -s '$bamFile2' two.bam &&
        #if $bamFile2.ext == 'bam':
            ln -s '${bamFile2.metadata.bam_index}' two.bam.bai &&
        #else:
            ln -s '${bamFile2.metadata.cram_index}' two.bam.crai &&
        #end if

        bamCompare
            --numberOfProcessors "\${GALAXY_SLOTS:-4}"
            --bamfile1 one.bam
            --bamfile2 two.bam

            --outFileName '$outFileName'
            --outFileFormat '$outFileFormat'

            --binSize $binSize

            #if $scaling.method == 'SES':
                --scaleFactorsMethod SES
                --sampleLength $scaling.sampleLength
                --numberOfSamples $scaling.numberOfSamples
            #elif $scaling.method == 'readCount':
                --scaleFactorsMethod readCount
            #elif $scaling.method == 'own':
                --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
            #elif $scaling.method == 'None':
                --scaleFactorsMethod None
                #if $scaling.type != '':
                    --normalizeUsing $scaling.type
                #end if
            #end if

            --operation $comparison.type
            $exactScaling

            #if $comparison.type in ['ratio','log2']:
                --pseudocount $comparison.pseudocount
            #end if

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

            #if $advancedOpt.showAdvancedOpt == "yes":
                #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
                $advancedOpt.skipZeroOverZero

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
                #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 bamFile1: bowtie2 test1.bam
bamFile2: bowtie2 test1.bam
binSize: 5
comparison|type: ratio
outFileFormat: bedgraph
advancedOpt|showAdvancedOpt: no
name: value
bowtie2 test1.bam
value
Test-2 bamFile1: bowtie2 test1.bam
bamFile2: bowtie2 test1.bam
binSize: 10
comparison|type: ratio
outFileFormat: bigwig
advancedOpt|showAdvancedOpt: yes
name: value
bowtie2 test1.bam
value