comparison hicPlotViewpoint.xml @ 5:67bd57e960a3 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287

4:c4f273c3c73f

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        hicPlotViewpoint --matrix '$matrix_h5_cooler'
        #if $interactionOutFileName:
            $interactionOutFileName interactions.bedgraph
        #end if
        --outFileName plot.$image_file_format
        --region $region
        --referencePoint $referencePoint
        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <expand macro="region" />
        <param name="referencePoint" type="text" label="Reference point"
            help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>

        <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"

        </param>

    </inputs>
    <outputs>

        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="png" format="png" />
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>
        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
            <filter>interactionOutFileName</filter>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000' />
            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000-3300000' />
            <param name='interactionOutFileName' value='True' />
            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
            <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>

        </test>
    </tests>
    <help><![CDATA[
Plot Viewpoint
==============

5:67bd57e960a3

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' ${counter}_matrix &&
        #end for
        #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        hicPlotViewpoint --matrix "$m"
        #if $interactionOutFileName:
            $interactionOutFileName interactions
        #end if
        --outFileName plot.$image_file_format
        --region $region
        --referencePoint $referencePoint
        && mv plot.$image_file_format plot
        && ls -lah
        #if $interactionOutFileName:
            #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
                && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph
            #end for
        #end if
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_macro' />
        <expand macro="region" />
        <param name="referencePoint" type="text" label="Reference point"
            help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>

        <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"

        </param>

    </inputs>
    <outputs>

        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="png" format="png" />
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>

        <data format="bedgraph" name="interactionFile" >
            <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
            <filter>interactionOutFileName</filter>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000' />
            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000-3300000' />
            <param name='interactionOutFileName' value='True' />
            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
            <output name="interactionFile">
                <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" />
            </output>
        </test>
    </tests>
    <help><![CDATA[
Plot Viewpoint
==============