annotate hcluster_sg.xml @ 1:09955cea320f draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 978a8efb9969646b97873d69348971860f2793f5

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

.. _hcluster_sg: https://github.com/douglasgscofield/hcluster
]]>
    </help>
    <citations>
    </citations>
</tool>