<tool id="mothur_count_seqs" name="Count.seqs" version="1.20.0" >
 <description>counts the number of sequences represented by the representative</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='count.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.seq.count$:'$seq_count
  --outputdir='$logfile.extra_files_path'
  --name=$name
  #if $grouping.use:
   #if $grouping.group.__str__ != "None" and len($grouping.group.__str__) > 0:
    --group='$grouping.group'
   #end if
   #if $grouping.groups.__str__ != "None" and len($grouping.groups.__str__) > 0:
    --groups='$grouping.groups'
   #end if
  #end if
 </command>
 <inputs>
  <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
  <conditional name="grouping">
   <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Use a Group file to include counts for groups"/>
   <when value="yes">
   <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
   <param name="groups" type="select" label="groups - Groups to display" multiple="true">
    <help>All groups displayed if none are selected.</help>
    <options from_dataset="group">
     <column name="name" index="1"/>
     <column name="value" index="1"/>
     <filter type="unique_value" name="unq_grp" column="1" />
    </options>
   </param>
   </when>
   <when value="no"/>
  </conditional> <!-- use_groups -->
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="seq_count" label="${tool.name} on ${on_string}: seq.count" />
 </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**

The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file. If a group_ file is given, it will also provide the group count breakdown.

.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _count.seqs: http://www.mothur.org/wiki/Count.seqs

 </help>
</tool>