annotate mcl.xml @ 0:4d1e4e729ae4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mcl commit dcb4abd1fcf9114ced686c7343c2de4b064a57c1

<tool id="mcl_clustering" name="MCL"  version="14.137">
    <description>A Markov Cluster Algorithm.</description>
    <xrefs>
        <xref type="bio.tools">mcl</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="14.137">mcl</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
    mcl
        $infile
        --abc
        -I $inflation
        -o $outfile
        -scheme $scheme
        -pi $pi
        -ph $ph
        -if $if
        --discard-loops=$discard_loops
]]>
    </command>
        <inputs>
            <param name="infile" type="data" format="tabular" label="MCL Label input"/>

            <param name="inflation" type="float" value="4.0" label="Main inflation value (-I)"
                help="This value is the main handle for affecting cluster granularity. It is usually chosen somewhere in the range [1.2-5.0]. -I 5.0 will tend to result in fine-grained clusterings, and -I 1.2 will tend to result in very coarse grained clusterings."/>
            <param name="pi" type="float" label="pre-inflation (-pi)" value="3.0" help=""/>
            <param name="ph" type="float" label="pre-inflation, max-bound (-ph)" value="3.0" help=""/>
            <param name="if" type="float" label="start-inflation (-if)" value="3.0" help=""/>

            <param name="discard_loops" truevalue="y" falsevalue="n" checked="True" type="boolean"
                label="remove any loops that are present in the input" help=""/>

            <param name="scheme" type="select" label="Resource schemes (-scheme)"
                help="High schemes result in more expensive computations that may possibly be more accurate.">
                <option value="1">1</option>
                <option value="2">2</option>
                <option value="3">3</option>
                <option value="4" selected="true">4</option>
                <option value="5">5</option>
                <option value="6">6</option>
                <option value="7">7</option>
            </param>

        </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="MCS on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="sample_input.tabular" ftype="tabular" />
            <param name="inflation" value="2.0" />
            <param name="scheme" value="4" />
            <output name="outfile" file="mcl_result_01.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

The Markov Cluster Algorithm, aka the MCL algorithm.

This program implements mcl, a cluster algorithm for graphs.
A single parameter controls the granularity of the output clustering, namely the -I inflation option described further below.
In standard usage of the program this parameter is the only one that may require changing.
By default it is set to 2.0 and this is a good way to start. If you want to explore cluster structure in graphs with MCL,
vary this parameter to obtain clusterings at different levels of granularity. A good set of starting values is 1.4, 2, 4, and 6.

**Example input (Label input)**

::

    cat hat 0.2
    hat bat 0.16
    bat cat 1.0
    bat bit 0.125
    bit fit 0.25
    fit hit 0.5
    hit bit 0.16

]]>
    </help>
    <creator>
        <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
        <person givenName="Pavankumar" familyName="Videm" url="https://github.com/pavanvidem" />
    </creator>
    <citations>
        <citation type="doi">10.1137/040608635</citation>
    </citations>
</tool>