annotate mothur/tools/mothur/deunique.tree.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

<tool id="mothur_deunique_tree" name="Deunique.tree" version="1.20.0">
 <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='deunique.tree'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.deunique\.tre$:'$out_tree
  --outputdir='$logfile.extra_files_path'
  --tree=$tree
  --name=$names
 </command>
 <inputs>
  <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
  <param name="names" type="data" format="names" label="names - Sequences Name reference"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" />
 </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 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


 </help>
</tool>