<tool id="mothur_make_design" name="Make Design" version="1.19.0" >
 <description>Assign groups to Sets</description>
 <command> cat $generated_design > $design
 </command>
 <inputs>
  <param name="source" type="data" format="shared,groups" label="Source containing groups"/>
    <repeat name="groupings" title="Grouping">
     <param name="name" type="text" label="Name for a new combined grouping"/>
     <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
      <options from_dataset="source">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
    </repeat>
 </inputs>
 <configfiles>
  <configfile name="generated_design">
#for $grouping in $groupings:
#set grp_str = $grouping.groups.__str__
#if grp_str != None and len(grp_str) > 0:
#for $grp in grp_str.split(','):
$grp	$grouping.name
#end for
#end if
#end for
  </configfile>
 </configfiles>
 <outputs>
  <data format="design" name="design" label="${tool.name} on ${on_string}: design" />
 </outputs>
 <requirements>
  <requirement type="binary">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**

Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.

.. _merge.groups: http://www.mothur.org/wiki/Merge.groups
.. _indicator: http://www.mothur.org/wiki/Indicator
.. _metastats: http://www.mothur.org/wiki/Metastats

 </help>
</tool>