<tool profile="16.07" id="mothur_metastats" name="Metastats" version="@WRAPPER_VERSION@.0">
    <description>generate principle components plot data</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 '$otu' otu.dat &&
ln -s '$design' design.dat &&

echo 'metastats(
    shared=otu.dat,
    design=design.dat,
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    #if $sets:
        sets=${ str($sets).replace(",","-") },
    #end if
    iters=$iters,
    threshold=$threshold,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
            <options>
                <filter type="data_meta" ref="design" key="groups"/>
            </options>
        </param>
        <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
        <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="design" value="toymothur.design2" ftype="mothur.design"/>
            <output_collection name="metastats" count="36">
                <element name="0.23.tardis_dalek" ftype="txt">
                    <assert_contents>
                        <has_text text="group1"/>
                        <has_text text="group2"/>
                        <has_text text="OTU"/>
                        <has_text text="variance"/>
                        <has_text text="1000 permutations"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="design" value="toymothur.design2" ftype="mothur.design"/>
            <param name="iters" value="42"/>
            <param name="threshold" value="0.1"/>
            <param name="label" value="0.03,0.05,0.23"/>
            <param name="groups" value="forest,pasture"/>
            <param name="sets" value="tardis,dalek"/>
            <output_collection name="metastats" count="3">
                <element name="0.23.tardis_dalek" ftype="txt">
                    <assert_contents>
                        <has_text text="group1"/>
                        <has_text text="group2"/>
                        <has_text text="OTU"/>
                        <has_text text="variance"/>
                        <has_text text="42 permutations"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The metastats_ command generate principle components plot data.

.. _metastats: https://www.mothur.org/wiki/Metastats

v.1.21.0: Updated to mothur 1.33

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pcbi.1000352</citation>
    </expand>
</tool>