<tool id="mothur_shhh_seqs" name="Shhh.seqs" version="1.23.0">
 <description>Denoise program (Quince SeqNoise)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='shhh.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh\.fasta$:'$shhh_fasta,'^\S+\.shhh\.names$:'$shhh_names,'^\S+\.shhh\.map$:'$shhh_map
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --name=$name
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group=$group
  #end if
  #if $sigma.__str__ != '':
   --sigma=$sigma 
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
  <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/>
  <param name="sigma" type="float" value="" optional="true" label="sigma" 
         help="default .01">
   <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
  <data format_source="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
  <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/>
 </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 shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.

.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs


 </help>
</tool>