comparison heatmapper.xml @ 65:9bee2c86eeb1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

64:627004611e98

<tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">heatmapper</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
<![CDATA[
        heatmapper

        --matrixFile $matrixFile

            --startLabel '$advancedOpt.startLabel' 
            --endLabel '$advancedOpt.endLabel'
            --refPointLabel '$advancedOpt.referencePointLabel'
            --regionsLabel '$advancedOpt.regionsLabel'

            #if str($advancedOpt.plotTitle.value) != "None":
                --plotTitle '$advancedOpt.plotTitle'
            #end if

            $advancedOpt.onePlotPerGroup

                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>
                <param name="plotTitle" type="text" value="" size="30"
                    label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" />
                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 
                    label="Do one plot per group" 
                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>

                <expand macro="kmeans_clustering" />

        <expand macro="output_graphic_outputs" />
        <expand macro="output_save_matrix_values" />
    </outputs>
    <tests>
        <test>
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
        </test>
    </tests>
    <help>
<![CDATA[

65:9bee2c86eeb1

<tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <macros>
        <token name="@BINARY@">heatmapper</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        heatmapper

        --matrixFile $matrixFile

            --startLabel '$advancedOpt.startLabel' 
            --endLabel '$advancedOpt.endLabel'
            --refPointLabel '$advancedOpt.referencePointLabel'
            --regionsLabel '$advancedOpt.regionsLabel'

            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                --plotTitle '$advancedOpt.plotTitle'
            #end if

            $advancedOpt.onePlotPerGroup

                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>
                <expand macro="plotTitle" />
                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 
                    label="Do one plot per group" 
                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>

                <expand macro="kmeans_clustering" />

        <expand macro="output_graphic_outputs" />
        <expand macro="output_save_matrix_values" />
    </outputs>
    <tests>
        <test>
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
        </test>
    </tests>
    <help>
<![CDATA[