<tool profile="16.07" id="mothur_otu_hierarchy" name="Otu.hierarchy" version="@WRAPPER_VERSION@.0">
    <description>Relate OTUs at different distances</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 'otu.hierarchy(
            list=otu.dat,
            label=$label1-$label2,
            output=$output
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="label1" type="select" label="label - OTU Label 1">
            <expand macro="labeloptions"/>
        </param>
        <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
            <expand macro="labeloptions"/>
        </param>
        <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
            <option value="name" selected="true">OTU sequence names</option>
            <option value="number">OTU numbers</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="label1" value="0.05"/>
            <param name="label2" value="0.03"/>
            <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The otu.hierarchy_ command relates OTUs from a list_ at different distances.

.. _list: https://www.mothur.org/wiki/List_file
.. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy

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