comparison correctGCBias.xml @ 66:1dbd76a58d8b draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty

65:9bee2c86eeb1

            #end if

            #if str($region).strip() != '':
                --region '$region'
            #end if
            --correctedFile $outFileName
]]>
    </command>
    <inputs>
        <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
        <param name="bamInput" format="bam" type="data"

        <data format="bam" name="outFileName" />
    </outputs>
    <tests>
        <test>
            <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="ref_source" value="history" />
            <param name="input1" value="phiX.2bit" />
            <param name="effectiveGenomeSize_opt" value="specific" />
            <param name="effectiveGenomeSize" value="5386" />
            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

66:1dbd76a58d8b

            #end if

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

        <data format="bam" name="outFileName" />
    </outputs>
    <tests>
        <test>
            <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
            <param name="ref_source" value="history" />
            <param name="input1" value="sequence.2bit" />
            <param name="effectiveGenomeSize_opt" value="specific" />
            <param name="effectiveGenomeSize" value="23011544" />
            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**