<tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0">
 <description>Trim sequences to a specified length</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chop.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.chop\.fasta$:'$out_fasta
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --numbases=$numbases
  --keep=$keep
  $countgaps
  $short
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/>
  <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
  <param name="keep" type="select" label="keep - Part of the sequence to keep">
   <option value="front">front</option>
   <option value="back">back</option>
  </param>
  <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/>
  <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" />
 </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 chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.

.. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs


 </help>
</tool>