<tool id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="1.27.0">
 <description>fraction of OTUs for samples or abundances</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__, "'^\S+\.core\.microbiome$:'" + $core_microbiome.__str__]
  --cmd='get.coremicrobiome'
  --outputdir='$logfile.extra_files_path'
  #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=$groups
  #end if
  #if len($abundance.__str__) > 0 or len($samples.__str__) > 0:
   #if len($abundance.__str__) > 0:
    --abundance=$abundance
   #end if
   #if len($samples.__str__) > 0:
    --samples=$samples
   #end if
   #set results = $results + ["'^\S+\.core\.microbiomelist$:'" + $core_microbiomelist.__str__]
  #end if
  --result=#echo ','.join($results)
 </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>
  <param name="abundance" type="integer" optional="true" label="abundance - list OTU names at this abundance">
   <validator type="in_range" message="abundance is between 0 and 100" min="0" max="100"/>
  </param>
  <param name="samples" type="integer" optional="true" label="samples - minimum number of samples requied to list OTU names">
   <validator type="in_range" message="between 1 and number of samples in your file" min="1"/>
  </param>
  <param name="output" type="select" label="output - fraction or count">
    <option value="fraction" selected="true">fraction</option>
    <option value="count">count</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="core_microbiome" label="${tool.name} on ${on_string}: core.microbiome"/>
  <data format="tabular" name="core_microbiomelist" label="${tool.name} on ${on_string}: core.microbiomelist">
    <filter>(len(abundance.__str__) > 0 or len(samples.__str__) > 0)</filter>
  </data>
 </outputs>
 <requirements>
   <requirement type="package" version="1.33">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.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.

.. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome

v1.27.0: Updated to Mothur 1.33


 </help>
</tool>