comparison hicAggregateContacts.xml @ 13:f0216498a666 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

12:e30485c5e93b

    #end if

    #if $vMax:
        --vMax $vMax
    #end if

    --outFileName plot.$image_file_format
    &&
    mv plot.$image_file_format plot
    #if $outputs and 'outFileObsExp' in $outputs:
        && mv 'ObsExp.$matrix_h5_cooler.ext' matrix
    #end if

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
        <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />

        <expand macro='range' />
        <param argument="--mode" type="select" label="Regions to consider.">
            <option value="inter-chr">inter-chr</option>
            <option value="intra-chr">intra-chr</option>
            <option value="all" selected="true">all</option>
        </param>

        <param argument="--operationType" type="select" label="Type of operation to compute final matrix">
            <option value="median" selected="true">median</option>
            <option value="mean">mean</option>
            <option value="sum">sum</option>
        </param>

        <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 
                           a bin of the input matrix, by default only the first bin 
                           is taken into account. However there are more posibilities 
                           to handel such a case. Users can ask for the last bin or 

        </collection>
        <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Heatmap">
            <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>
        <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <filter>'outFileObsExp' in outputs</filter>
            <change_format>
                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
            <param name="numberOfBins" value="30" />
            <param name="range_max" value="900000" />
            <param name="range_min" value="50000" />

13:f0216498a666

    #end if

    #if $vMax:
        --vMax $vMax
    #end if
 
    $considerStrandDirection
 
    --outFileName plot.$image_file_format
    &&
    mv plot.$image_file_format plot
    #if $outputs and 'outFileObsExp' in $outputs:
        && mv 'ObsExp.$matrix_h5_cooler.ext' matrix
    #end if

]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
        <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />

        <expand macro="range" />
        <param argument="--mode" type="select" label="Regions to consider.">
            <option value="inter-chr">inter-chr</option>
            <option value="intra-chr">intra-chr</option>
            <option value="all" selected="true">all</option>
        </param>

        <param argument="--operationType" type="select" label="Type of operation to compute final matrix">
            <option value="median" selected="true">median</option>
            <option value="mean">mean</option>
            <option value="sum">sum</option>
        </param>
        <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />

        <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 
                           a bin of the input matrix, by default only the first bin 
                           is taken into account. However there are more posibilities 
                           to handel such a case. Users can ask for the last bin or 

        </collection>
        <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Heatmap">
            <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>
        <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <filter>outputs == 'outFileObsExp'</filter>
            <change_format>
                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
            <param name="numberOfBins" value="30" />
            <param name="range_max" value="900000" />
            <param name="range_min" value="50000" />