view tools/mothur/deunique.tree.xml @ 0:ee4fee239fe7 draft default tip

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<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="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'deunique.tree(
            tree=$tree,
            name=$names
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        prefix="$tree" &&
        mv mothur.*.logfile "$logfile" &&
        mv \${prefix%.dat}*.deunique.tre "$out_tree"
    ]]></command>
    <inputs>
        <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
        <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="out_tree" format_source="tree" label="${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"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documenation**

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

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

v1.21.0: Updated to Mothur 1.33

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