<tool profile="16.07" id="mothur_pca" name="Pca" version="@WRAPPER_VERSION@.0">
    <description>Principal Coordinate Analysis for a shared file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$otu' otu.dat &&

echo 'pca(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat,
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    metric=$metric
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="pca_axes" type="list" label="${tool.name} on ${on_string}: pca.axes">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.axes" format="mothur.axes"/>
        </collection>
        <collection name="pca_loadings" type="list" label="${tool.name} on ${on_string}: pca.loadings">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.loadings" format="txt"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="groups" value="forest,pasture"/>
            <param name="label" value="0.22,0.55"/>
            <output_collection name="pca_axes" count="2">
                <element name="0.22" md5="4e32155fcfefe7d2f45b896d26b36409" ftype="mothur.axes"/>
            </output_collection>
            <output_collection name="pca_loadings" count="2">
                <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The pca_ command generate principle components plot data for a shared_ or relabund_ file.

.. _shared: https://www.mothur.org/wiki/Shared_file
.. _relabund: https://www.mothur.org/wiki/Get.relabund
.. _pca: https://www.mothur.org/wiki/Pca

    ]]></help>
    <expand macro="citations">
        <expand macro="citations-ecology"/>
    </expand>
</tool>