annotate mothur/tools/mothur/split.groups.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

<tool id="mothur_split_groups" name="Split.groups" version="1.20.0" force_history_refresh="True">
 <description>Generates a fasta file for each group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='split.groups'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.names)$:names'
  --fasta=$fasta
  --group=$group
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name=$name
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
  <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/>
  <param name="group" type="data" format="groups" label="group - Groups"/>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
   <options>
    <filter type="data_meta" ref="group" key="groups" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.

.. _group: http://www.mothur.org/wiki/Group_file
.. _name: http://www.mothur.org/wiki/Name_file
.. _split.groups: http://www.mothur.org/wiki/Split.groups

 </help>
</tool>