comparison correctGCBias.xml @ 24:d7c9fd76e41e draft

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23:8c452f37c896

        ###set newoutFileName="corrected."+str($outFileFormat)
        ##--correctedFile $newoutFileName;
        --correctedFile "corrected.bam";

        mv $newoutFileName $outFileName
    </command>
    <inputs>
        <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
        <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
        <expand macro="reference_genome_source" />

    </outputs>
    <help>

**What it does**

This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res.
The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.


You can find more details in the `correctGCBias wiki`_.

.. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias


**Output files**:

- GC-normalized BAM file

24:d7c9fd76e41e

        ###set newoutFileName="corrected."+str($outFileFormat)
        ##--correctedFile $newoutFileName;
        --correctedFile "corrected.bam";

        mv "corrected.bam" $outFileName
    </command>
    <inputs>
        <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
        <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
        <expand macro="reference_genome_source" />

    </outputs>
    <help>

**What it does**

This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
Benjamini and Speed (2012) Nucleic Acids Res.
The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.

You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias


**Output files**:

- GC-normalized BAM file