annotate mothur/tools/mothur/list.otulabels.xml @ 33:d53b9eb16c2d

mothur_wrapper.py - convert_value needs to return a String

<tool id="mothur_list_otulabels" name="List.otulabels" version="1.26.0">
 <description>Lists otu labels from shared or relabund file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='list.otulabels'
  --outputdir='$logfile.extra_files_path'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otulabels$:'$otulabels
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
   --relabund=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label=$label
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="otulabels" name="otulabels" label="${tool.name} on ${on_string}: otulabels"/>
 </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 list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands.

.. _list.otulabels: http://www.mothur.org/wiki/List.otulabels
.. _classify.otu: http://www.mothur.org/wiki/Classify.otu
.. _otu.association: http://www.mothur.org/wiki/Otu.association
.. _corr.axes: http://www.mothur.org/wiki/Corr.axes
.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels
.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _relabund: http://www.mothur.org/wiki/Get.relabund


 </help>
</tool>