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author matnguyen
date Mon, 11 Mar 2019 12:46:41 -0400
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<tool id="consensus_clustering" name="PathOGiST - Consensus Clustering" version="1.0.0">
    <description>: Performs consensus clustering on multiple clusterings</description>
    <requirements>
        <requirement type="package" version="0.3">pathogist</requirement>
    </requirements>

    <command><![CDATA[
        PATHOGIST consensus $constraints $distances $clusterings $fine_clusterings cc.tsv
    ]]></command>

    <inputs>
        <param name="distances" type="data" format="tabular,txt" label="Distance Matrices"
               help="File contains paths to distance matrices for different clusterings"/>
        <param name="clusterings" type="data" format="tabular,txt" label="Clusterings"
               help="File contains paths to clusterings (matrices or lists of clustering assignments)"/>
        <param name="fine_clusterings" type="data" format="tabular,txt" label="Fine Clusterings"
               help="File contains names of the clusterings which are the finest"/>
        <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="Consensus clustering on ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
    </outputs>

    <help>

    </help>

    <citations>

    </citations>
</tool>