comparison plotPCA.xml @ 14:dfe535b75616 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28

13:fec11d9764c7

        @BINARY@
            --corData "$corData"
            --plotTitle "$plotTitle"
            --plotFile "$outFileName"
            --plotFileFormat "$outFileFormat"
            $rowCenter
            #if $outFileNameData
                --outFileNameData "$output_outFileNameData"
            #end if
]]>

        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
        <expand macro="input_image_file_format" />
        <expand macro="plotTitle" />
        <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
        <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically." truevalue="--rowCenter" falsevalue="" />
    </inputs>
    <outputs>
        <expand macro="output_image_file_format_not_nested" />
        <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
            <filter>outFileNameData</filter>

14:dfe535b75616

        @BINARY@
            --corData "$corData"
            --plotTitle "$plotTitle"
            --plotFile "$outFileName"
            --plotFileFormat "$outFileFormat"
            #if str($advancedOpt.showAdvancedOpt) == 'yes':
                @PLOTWIDTHHEIGHT@
            #end if
            $rowCenter
            #if $outFileNameData
                --outFileNameData "$output_outFileNameData"
            #end if
]]>

        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
        <expand macro="input_image_file_format" />
        <expand macro="plotTitle" />
        <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
        <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically." truevalue="--rowCenter" falsevalue="" />
        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="output_image_file_format_not_nested" />
        <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
            <filter>outFileNameData</filter>