<tool id="mothur_classify_tree" name="Classify.tree" version="1.24.0">
 <description>Get a consensus taxonomy for each node on a tree</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.tree'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy\.tre$:'$out_tree,'^\S+\.taxonomy\.summary$:'$summary
  --outputdir='$logfile.extra_files_path'
  --taxonomy=$taxonomy
  --tree=$tree
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group=$group
  #end if

  --name=$names
 </command>
 <inputs>
  <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
  <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file"/>
  <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/>
  <param name="cutoff" type="integer" value="51" optional="true" label="cutoff - consensus confidence threshold" 
         help="The default is 51, meaning 51%. Cutoff cannot be below 51">
    <validator type="in_range" message="The percentage cutoff must be between 51 and 100" min="51" max="100"/>
  </param>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: taxonomy.tre" />
  <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

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


 </help>
</tool>