<tool id="mothur_otu_association" name="Otu.association" version="1.24.0" force_history_refresh="True">
 <description>Calculate the correlation coefficient for the otus</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='otu.association'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.norm\.shared$:'$shared
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.otu.corr$:$tabular'
  #if isinstance($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
  #if $method.__str__ != "None" and len($method.__str__) > 0:
   --method=$method
  #end if
  #if $metadata.__str__ != "None" and len($method.__str__) > 0:
   --metadata=$metadata
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to include" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
  <param name="method" type="select" label="method - Normalization method">
   <option value="pearson" selected="true">pearson</option>
   <option value="spearman">spearman</option>
   <option value="kendall">kendall</option>
  </param>
  <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${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 otu.association_ command calculates the correlation coefficient for the otus in a shared_ or relabund_ file.

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _relabund: http://www.mothur.org/wiki/Get.relabund
.. _otu.association: http://www.mothur.org/wiki/Otu.association

 </help>
</tool>