<tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.20.0">
 <description>Relate OTUs at different distances</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  --cmd='otu.hierarchy'
  --outputdir='$logfile.extra_files_path'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otu\.hierarchy$:'$hierarchy
  --list=$list
  --label=$label1,$label2
  --output=$output
 </command>
 <inputs>
  <param name="list" type="data" format="list" label="list - OTU List"/>
  <param name="label1" type="select" label="label - OTU Label 1" >
   <options>
    <filter type="data_meta" ref="list" key="labels" />
   </options>
  </param>
  <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
   <options>
    <filter type="data_meta" ref="list" key="labels" />
   </options>
  </param>
  <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
   <option value="name" selected="treu">OTU sequence names</option>
   <option value="number">OTU numbers</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">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 otu.hierarchy_ command relates OTUs from a list_ at different distances.

.. _list: http://www.mothur.org/wiki/List_file
.. _otu.hierarchy: http://www.mothur.org/wiki/Otu.hierarchy


 </help>
</tool>