view tools/correlation_clustering/correlation_clustering.xml @ 0:6a73638d707c draft

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<tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0">
    <description>: Runs correlation clustering on a distance matrix file</description>
    <requirements>
        <requirement type="package" version="0.0.1">pathogist</requirement>
    </requirements>

    <command><![CDATA[
        PATHOGIST correlation $constraints $distance $threshold cc.tsv
    ]]></command>

    <inputs>
        <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/>
        <param name="threshold" type="integer" value="0" label="Threshold Value"
               help="The threshold value can be determined by visualizing the distance matrix"/>
        <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue=""
               label="All Constraints"
               help="Add all constraints to the optimization problem, not just those with mixed signs"/>
    </inputs>

    <outputs>
        <data name="clustering" label="Correlation clustering of ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
    </outputs>

    <help>

    </help>

    <citations>

    </citations>
</tool>