annotate mothur/tools/mothur/unique.seqs.xml @ 4:5265aa9067e0

set output formats to match input formats

<tool id="mothur_unique_seqs" name="Unique.seqs" version="1.19.0">
 <description>Return unique sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='unique.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.unique\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  #if $names.__str__ != "None" and len($names.__str__) > 0:
   --name=$names
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
  <param name="names" type="data" format="names" optional="true" label="names - Sequences Names"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
 </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 unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence. 

.. _name: http://www.mothur.org/wiki/Name_file
.. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs


 </help>
</tool>