<tool profile="16.07" id="mothur_mantel" name="Mantel" version="@WRAPPER_VERSION@.0">
    <description>Mantel correlation coefficient between two matrices.</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 '$dist' dist.dat &&
ln -s '$dist2' dist2.dat &&

echo 'mantel(
    phylip1=dist.dat,
    phylip2=dist2.dat,
    method=$method,
    iters=$iters
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="dist2" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
        <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
                <option value="pearson" selected="true">pearson</option>
                <option value="spearman">spearman</option>
                <option value="kendall">kendall</option>
        </param>
        <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/>
    </outputs>
    <tests>
        <test>
            <param name="dist" value="veg.dist"/>
            <param name="dist2" value="env.dist"/>
            <output name="mantel" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^Mantel\tpValue$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The mantel_ command calculates the Mantel correlation coefficient between two matrices_.

.. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _mantel: https://www.mothur.org/wiki/Mantel

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