<tool profile="16.07" id="mothur_classify_tree" name="Classify.tree" version="@WRAPPER_VERSION@.0">
    <description>Get a consensus taxonomy for each node on a 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 '$tree' tree.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
ln -s '$taxonomy' taxonomy.dat &&

echo 'classify.tree(
    tree=tree.dat,
    #if $name
        name=name.dat,
    #end if
    #if $group:
        group=group.dat,
    #end if
    taxonomy=taxonomy.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
        <param argument="tree" type="data" format="txt" label="tree - Sequences to filter"/>
        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/>
        <param argument="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold"
            help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
        <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
    </outputs>
    <tests>
        <test>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
            <param name="tree" value="treetest.tre" ftype="txt"/>
            <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
            <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The classify.tree_ command is used to get a consensus taxonomy for each node on a tree.
Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
The output is a tree_ and a summary..

  TreeNode  NumRep  Taxonomy
  243   2   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
  244   3   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
  245   4   Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
  ...


.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
.. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
.. _name: https://www.mothur.org/wiki/Name_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _classify.tree: https://www.mothur.org/wiki/Classify.tree

v.1.25.0: Trivial upgrade to Mothur 1.33

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