comparison bamCoverage.xml @ 6:1a9fad4988f3 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

5:8c6f450d266c

                #end if

                @ADVANCED_OPTS_READ_PROCESSING@
                $advancedOpt.skipNAs

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                #end if
            #end if
]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>

        <param name="binSize" type="integer" value="50" min="1"
            label="Bin size in bp"
            help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>

        <conditional name="scaling">
            <param name="type" type="select" label="Scaling/Normalization method" >

            <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help>

fragment length.

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCoverage.html


**Output files**:

- coverage file either in bigWig or bedGraph format

6:1a9fad4988f3

                #end if

                @ADVANCED_OPTS_READ_PROCESSING@
                $advancedOpt.skipNAs

                if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                end if
            #end if
]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>

        <param name="binSize" type="integer" value="50" min="1" 
            label="Bin size in bp"
            help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>

        <conditional name="scaling">
            <param name="type" type="select" label="Scaling/Normalization method" >

            <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="no" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help>

fragment length.

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage


**Output files**:

- coverage file either in bigWig or bedGraph format