Repository revision
29:3d211717a775

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

bigwigCompare tool metadata
Miscellaneous
normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them
deeptools_bigwig_compare
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.2+galaxy0
3.5.2+galaxy0
bigwigCompare --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.0.1.0
deeptools_bigwig_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
bigwigCompare
            --numberOfProcessors "\${GALAXY_SLOTS:-4}"
            --bigwig1 '$bigwigFile1'
            --bigwig2 '$bigwigFile2'

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

            --operation $comparison.comparison_select

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

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

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

              $advancedOpt.skipNAs
              $advancedOpt.skipZeroOverZero
              --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
              --binSize $advancedOpt.binSize

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #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 bigwigFile1: test.bw
bigwigFile2: test.bw
comparison|comparison_select: ratio
outFileFormat: bigwig
advancedOpt|showAdvancedOpt: no
name: value
test.bw
value
Test-2 bigwigFile1: test.bw
bigwigFile2: test.bw
comparison|comparison_select: ratio
outFileFormat: bedgraph
advancedOpt|showAdvancedOpt: no
name: value
test.bw
value