<tool profile="16.07" id="mothur_libshuff" name="Libshuff" version="@WRAPPER_VERSION@.0">
    <description>Cramer-von Mises tests communities for the same structure</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 '$dist' dist.dat &&
ln -s '$group' group.dat &&

echo 'libshuff(
    phylip=dist.dat,
    group=group.dat,
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    sim=$sim,
    #if $form.form2 == "discrete":
        step=$form.step,
        #if $form.cutoff:
            cutoff=$form.cutoff,
        #end if
    #end if
    iters=$iters
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
        <param name="groups" type="select" multiple="true" label="groups - Groups to condider">
            <options>
                <filter type="data_meta" ref="group" key="groups"/>
            </options>
        </param>
        <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
        <conditional name="form">
            <param name="form2" type="select" label="form - Select a Clustering Method" help="">
                <option value="integral" selected="true">Integral</option>
                <option value="discrete">Discrete</option>
            </param>
            <when value="integral"/>
            <when value="discrete">
                <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
                <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
        <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>
    </outputs>
    <tests>
        <test>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <output name="summary">
                <assert_contents>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <output name="coverage">
                <assert_contents>
                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="forest,pasture"/>
            <param name="form2" value="discrete"/>
            <param name="step" value="0.25"/>
            <param name="cutoff" value="0.25"/>
            <output name="summary">
                <assert_contents>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <output name="coverage">
                <assert_contents>
                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.

.. _libshuff: https://www.mothur.org/wiki/Libshuff

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1128/AEM.67.9.4374-4376.2001</citation>
        <citation type="doi">10.1128/AEM.70.9.5485-5492.2004</citation>
    </expand>
</tool>