<tool id="mothur_make_biom" name="Make.biom" version="1.25.0" force_history_refresh="True">
 <description>Make biom files from a shared file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='make.biom'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.((\S+)\.biom)$:biom'
  --shared=$shared
  #if $contaxonomy != 'none' and len($contaxonomy.__str__) > 0:
   --contaxonomy=$contaxonomy
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
  #end if
  --matrixtype=$matrixtype
 </command>
 <inputs>
  <param name="shared" type="data" format="shared" label="shared - OTU Shared file"/>
  <param name="contaxonomy" type="data" format="cons.taxonomy" label="contaxonomy - consensus taxonomy"
         help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
  <param name="matrixtype" type="select" label="matrixtype - sparse or dense">
    <option value="sparse">sparse</option>
    <option value="dense">dense</option>
  </param>
  <param name="groups" type="select" label="groups - Groups to include" multiple="true"
     help="By default all are included if no selection is made.">
   <options>
    <filter type="data_meta" ref="shared" key="groups" />
   </options>
  </param>
  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
     help="By default all are included if no selection is made.">
   <options>
    <filter type="data_meta" ref="shared" key="labels" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 make.biom command converts a shared_ shared file to biom_ files. 
The output can be filtered by groups and labels.


.. _shared: http://www.mothur.org/wiki/Shared_file
.. _biom:  http://biom-format.org/documentation/biom_format.html
.. _make.biom: http://www.mothur.org/wiki/Make.biom

 </help>
</tool>