comparison mothur/tools/mothur/cluster.fragments.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

0:3202a38e44d9

<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.15.0">
 <description> Group sequences that are part of a larger sequence</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.fragments'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --name=$names
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
  <param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="out_fasta" label="${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 cluster.fragments_ command groups sequences that are part of a larger sequence.

.. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments


 </help>
</tool>