Repository revision
29:5bffaa8354a1

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

correctGCBias tool metadata
Miscellaneous
uses the output from computeGCBias to generate GC-corrected BAM/CRAM files
deeptools_correct_gc_bias
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.2+galaxy0
3.5.2+galaxy0
correctGCBias --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.0.1.0
deeptools_correct_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

        correctGCBias
            --numberOfProcessors "\${GALAXY_SLOTS:-4}"
            --bamfile local_bamInput.bam
            --GCbiasFrequenciesFile '$GCbiasFrequenciesFile'

            
    #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
            --correctedFile corrected.bam

    
None
False
Functional tests
name inputs outputs required files
Test-1 GCbiasFrequenciesFile: computeGCBias_result1.tabular
bamInput: paired_chr2L.bam
source|input1: sequence.2bit
source|ref_source: history
effectiveGenomeSize|effectiveGenomeSize: 10050
effectiveGenomeSize|effectiveGenomeSize_opt: specific
name: value
computeGCBias_result1.tabular
paired_chr2L.bam
sequence.2bit
value