view tools/mothur/pcoa.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

<tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0">
    <description>Principal Coordinate Analysis for a distance matrix</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'pcoa(
            phylip=$phylip,
            metric=$metric
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        prefix="$phylip" &&
        mv mothur.*.logfile "$logfile" &&
        mv \${prefix%.dat}*.pcoa.axes "$pcoa" &&
        mv \${prefix%.dat}*.pcoa.loadings "$loadings"
    ]]></command>
    <inputs>
        <param name="phylip" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
        <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="pcoa" format="mothur.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
        <data name="loadings" format="tabular" label="${tool.name} on ${on_string}: loadings"/>
    </outputs>
    <tests>
        <test>
            <param name="phylip" value="amazon.dist"/>
            <output name="pcoa" file="amazon.pcoa.axes"/>
            <output name="loadings" file="amazon.pcoa.loadings"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.

.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _pcoa: http://www.mothur.org/wiki/Pcoa
]]>
    </help>
    <expand macro="citations"/>
</tool>