<tool id="mothur_summary_seqs" name="Summary.seqs" version="1.20.0">
 <description>Summarize the quality of sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$out_summary
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name=$name
  #end if

  #if $count.__str__ != "None" and len($count.__str__) > 0:
    --count=$count
  #end if

 --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/>
  <param name="name" type="data" format="names" label="name - Names" optional="true"/>
  <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" 
         help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" />
 </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 summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.


.. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs

 </help>
</tool>