<tool id="biomd_extract_clusters" name="Extract clusters of MD trajectories" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from linkage matrix data</description>
    <macros>
        <token name="@TOOL_VERSION@">1.5.2</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
        <requirement type="package" version="1.19.1">numpy</requirement>
        <requirement type="package" version="3.3.1">matplotlib</requirement>
    </requirements>
    <command><![CDATA[
        python '$__tool_directory__/get_clusters.py'
            --Z '$Z'
            --threshold '$threshold'
            --min-members '$min_members'
            --output '$output'
]]></command>
    <inputs>
        <param label="Clustering linkage array" format="tabular" type="data" name="Z" argument="--Z"/>
        <param label="Distance cutoff" value="0" type="integer" name="threshold" argument="--threshold"/>
        <param label="Minimum number of members of the cluster" value="0" type="integer" name="min_members" argument="--min-members"/>
    </inputs>
    <outputs>
        <data label="Cluster members (JSON)" format="json" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="Z" value="Z.tabular"/>
            <param name="threshold" value="2"/>
            <param name="min_members" value="2"/>
            <output name="output" value="clusters.json"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool takes the hierarchical clustering linkage array (in tabular format) produced by the 'Hierarchical clustering' tool and returns a list of clusters and their members in JSON format.

_____


.. class:: infomark

**Input**

       - Clustering linkage array.
       - User-selected distance threshold for clustering and minimum number of members a cluster must have to be returned.

_____


.. class:: infomark

**Output**

       - JSON file containing a list of clusters and their members.

    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41592-019-0686-2</citation>
        <citation type="doi">{10.1109/MCSE.2007.55</citation>
    </citations>
</tool>