comparison plotCorrelation.xml @ 33:f1518335ac27 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty

32:d97b5324b279

                @HEATMAP_OPTIONS@
                --plotWidth $plotting_type.plotWidth
                --plotHeight $plotting_type.plotHeight
            #else:
                --plotTitle '$plotting_type.plotTitle'
            #end if
            $skipZeros
            --plotFileFormat "$outFileFormat"
            $removeOutliers
            #if $outFileCorMatrix:

                <expand macro="heatmap_options" />
                <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" />
            </when>
            <when value="scatterplot">
                <expand macro="plotTitle" />
            </when>
        </conditional>

        <expand macro="skipZeros" />

        <test>
            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
            <param name="outFileFormat" value="png" />
            <param name="outFileCorMatrix" value="True" />
            <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />
        </test>
        <test>
            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
            <param name="outFileFormat" value="png" />
            <param name="whatToPlot" value="scatterplot" />

33:f1518335ac27

                @HEATMAP_OPTIONS@
                --plotWidth $plotting_type.plotWidth
                --plotHeight $plotting_type.plotHeight
            #else:
                --plotTitle '$plotting_type.plotTitle'
                #if str($plotting_type.maxRange) != '':
                    --maxRange '$plotting_type.maxRange'
                #end if
                $plotting_type.log1p
            #end if
            $skipZeros
            --plotFileFormat "$outFileFormat"
            $removeOutliers
            #if $outFileCorMatrix:

                <expand macro="heatmap_options" />
                <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" />
            </when>
            <when value="scatterplot">
                <expand macro="plotTitle" />
                <param argument="--maxRange" type="integer" value="" optional="true"
                    label="Maximum Range"
                    help="Maximum (integer) value for the X and Y axes. The default scales these such that the full range of dots is displayed. If you specify --log1p, please ensure that this value is within the range it will produce." />
                <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue=""
                    label="Log transform"
                    help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." />
            </when>
        </conditional>

        <expand macro="skipZeros" />

        <test>
            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
            <param name="outFileFormat" value="png" />
            <param name="outFileCorMatrix" value="True" />
            <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" />
        </test>
        <test>
            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
            <param name="outFileFormat" value="png" />
            <param name="whatToPlot" value="scatterplot" />