<tool id="hcluster_sg" name="hcluster_sg" version="0.5.1.1">
    <description>Hierarchically clustering on a sparse graph</description>
    <requirements>
        <requirement type="package" version="0.5.1">hcluster_sg</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
hcluster_sg
-w $w
$c_conditional.c
#if $c_conditional.c == ''
    -s $c_conditional.s
    -m $c_conditional.m
    -b $c_conditional.b
    $c_conditional.O.O_selector
    #if $c_conditional.O.O_selector == '-O'
        -r $c_conditional.O.r
    #end if
    #if $c_conditional.C
        -C '$c_conditional.C'
    #end if
    -L $c_conditional.L
#end if
'$inputFile'
> '$outputFile'
    ]]></command>
    <inputs>
        <param name="inputFile" type="data" format="tabular" label="Weight file" help="3-columns format: id-1 id-2 integer-weight" />
        <param argument="-w" type="integer" min="0" value="20" label="Minimum edge weight" />
        <conditional name="c_conditional">
            <param argument="-c" type="select" label="Only find single-linkage clusters" help="Bypass h-cluster">
                <option value="-c">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <when value="-c" />
            <when value="">
                <param argument="-s" type="float" value="0.5" label="Minimum edge density between a join" />
                <param argument="-m" type="integer" value="500" label="Maximum size" />
                <param argument="-b" type="float" value="0.1" label="Breaking edge density" />
                <conditional name="O">
                    <param name="O_selector" argument="-O" type="select" label="Use once-fail-inactive-forever mode">
                        <option value="-O">Yes</option>
                        <option value="" selected="true">No</option>
                    </param>
                    <when value="-O">
                        <param argument="-r" type="integer" value="5" label="Weight resolution" />
                    </when>
                    <when value="" />            
                </conditional>
                <param argument="-C" type="data" format="tabular" optional="true" label="Category file" />
                <param argument="-L" type="integer" value="2" label="Stringency level" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outputFile" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="inputFile" ftype="tabular" value="exam-1.txt" />
            <output name="outputFile" file="hcluster_sg1.txt" />
        </test>
        <test>
            <param name="inputFile" ftype="tabular" value="exam-1.txt" />
            <conditional name="c_conditional">
                <param name="c" value="-c" />
            </conditional>
            <output name="outputFile" file="hcluster_sg2.txt" />
        </test>
    </tests>
    <help><![CDATA[
`hcluster_sg`_ is a generic tool for hierarchical or single-linkage clustering on a sparse graph.
Used by the `Ensembl Compara GeneTrees`_ pipeline.

.. _hcluster_sg: https://github.com/douglasgscofield/hcluster
.. _Ensembl Compara GeneTrees: https://www.ensembl.org/info/genome/compara/homology_method.html
    ]]></help>
    <citations>
        <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
    </citations>
</tool>