<tool profile="16.07" id="mothur_deunique_tree" name="Deunique.tree" version="@WRAPPER_VERSION@.0">
    <description>Reinsert the redundant sequence identiers back into a unique tree.</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 '$tree' tree.dat &&
ln -s '$names' names.dat &&

echo 'deunique.tree(
    tree=tree.dat,
    name=names.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/>
        <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/>
    </outputs>
    <tests>
        <test>
            <param name="tree" value="treetest.tre"/>
            <param name="names" value="treetest.names"/>
            <output name="out_tree" file="treetest.deunique.tre"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.

.. _name: https://www.mothur.org/wiki/Name_file
.. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree

v1.21.0: Updated to Mothur 1.33

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