comparison bamCoverage.xml @ 37:2f7edf06a5da draft

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36:ea2f64efe70d

        --binSize $binSize

        #if $scaling.type=='rpkm':
            --normalizeUsingRPKM
        #elif $scaling.type=='1x':
            --normalizeTo1x $scaling.normalizeTo1x
        #elif $scaling.type=='own':
            --scaleFactor $scaling.scaleFactor
        #end if

        #if $advancedOpt.showAdvancedOpt == "yes":

                <option value="no">Do not normalize or scale</option>
            </param>
            <when value="rpkm"/>
            <when value="no"/>
            <when value="1x">
                <param name="normalizeTo1x" type="integer" value="2150570000"
                    label="Genome size"
                    help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
            </when>
            <when value="own">
                <param name="scaleFactor" type="float" value="1" size="3" 
                    label="Scale factor to multiply all values" />
            </when>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


**Output files**:

- coverage file either in bigWig or bedGraph format

-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>

37:2f7edf06a5da

        --binSize $binSize

        #if $scaling.type=='rpkm':
            --normalizeUsingRPKM
        #elif $scaling.type=='1x':
            #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
            #else:
                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
            #end if
        #elif $scaling.type=='own':
            --scaleFactor $scaling.scaleFactor
        #end if

        #if $advancedOpt.showAdvancedOpt == "yes":

                <option value="no">Do not normalize or scale</option>
            </param>
            <when value="rpkm"/>
            <when value="no"/>
            <when value="1x">
                <expand macro="effectiveGenomeSize" />
            </when>
            <when value="own">
                <param name="scaleFactor" type="float" value="1" size="3" 
                    label="Scale factor to multiply all values" />
            </when>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


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

.. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage


**Output files**:

- coverage file either in bigWig or bedGraph format

-----

@REFERENCES@

    </help>
</tool>