annotate mothur/tools/mothur/get.sabund.xml @ 27:49058b1f8d3f

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

<tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0">
 <description>Get sabund from a otu list or rabund</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='get.sabund'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund
  --outputdir='$logfile.extra_files_path'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label=$label
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/>
  <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
 </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 get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.

.. _sabund: http://www.mothur.org/wiki/Sabund_file
.. _list: http://www.mothur.org/wiki/List_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _get.sabund: http://www.mothur.org/wiki/Get.sabund


 </help>
</tool>