Repository revision
28:5be24eba848d

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

computeGCBias tool metadata
Miscellaneous
Determine the GC bias of your sequenced reads
deeptools_compute_gc_bias
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.2+galaxy0
3.5.2+galaxy0
computeGCBias --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.0.1.0
deeptools_compute_gc_bias
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' local_bamInput.bam &&
        #if $bamInput.ext == 'bam':
            ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai &&
        #else:
            ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai &&
        #end if

        computeGCBias
            --numberOfProcessors "\${GALAXY_SLOTS:-4}"
            --bamfile local_bamInput.bam
            --GCbiasFrequenciesFile $outFileName

            #if $fragmentLength != "":
                --fragmentLength $fragmentLength
            #end if

            
    #if $source.ref_source=="history":
        --genome $source.input1
    #else:
        --genome '$source.input1_2bit.fields.path'
    #end if
    

            #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
            #else:
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

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

            #if $advancedOpt.showAdvancedOpt == "yes":
                --sampleSize '$advancedOpt.sampleSize'
                --regionSize '$advancedOpt.regionSize'

                #if $advancedOpt.extraSampling:
                    --extraSampling $advancedOpt.extraSampling
                #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

            #if str($image_format) != 'none':
                --biasPlot $outImageName
                --plotFileFormat $image_format
            #end if

    
None
False
Functional tests
name inputs outputs required files
Test-1 bamInput: paired_chr2L.bam
source|input1: sequence.2bit
source|ref_source: history
effectiveGenomeSize|effectiveGenomeSize: 10050
effectiveGenomeSize|effectiveGenomeSize_opt: specific
fragmentLength: 300
region: chr2L
advancedOpt|sampleSize: 10
advancedOpt|regionSize: 1
advancedOpt|showAdvancedOpt: yes
image_format: none
name: value
paired_chr2L.bam
sequence.2bit
value