<tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0"  force_history_refresh="True">
 <description>Generate a fasta with a representative sequence for each OTU</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='get.oturep'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
  #end if
  --fasta=$fasta
  --list=$otu_list
  #if $input.source == 'column':
   --column=$input.dist
   --name=$input.name
  #elif $input.source == 'phylip':
   --phylip=$input.dist
   #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
    --name=$input.name
   #end if
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $pick.type == 'yes':
   #if $pick.group.__str__ != "None" and len($pick.group.__str__) > 0:
    --group=$pick.group
   #end if
   #if $pick.groups.__str__ != "None" and len($pick.groups.__str__) > 0:
    --groups=$pick.groups
   #end if
  #end if
  #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
   --sorted=$sorted
  #end if
  $large
 </command>
 <inputs>
  <!-- get.relabund  relabund type should also work -->
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
  <param name="otu_list" type="data" format="list" label="list - OTU List"/>
  <conditional name="input">
   <param name="source" type="select" label="Distance Matrix Format">
    <option value="column">Pairwise Column Distance Matrix</option>
    <option value="phylip">Phylip Distance Matrix</option>
   </param>
   <when value="column">
    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
    <param name="name" type="data" format="names" optional="true" label="name - Names"/>
   </when>
  </conditional>
  <conditional name="pick">
   <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
    <option value="no" selected="true">No</option>
    <option value="yes">Yes</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/>
    <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
     <options from_dataset="group">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
   </when>
  </conditional> <!-- pick -->
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu_list">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="sorted" type="select" label="sorted - Sort Sequences by">
   <option value="">Don't sort</option>
   <option value="name">Sequence Name</option>
   <option value="number">Bin Number</option>
   <option value="size">Bin Size</option>
   <option value="group">Group</option>
  </param>
  <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>
 <requirements>
  <requirement type="binary">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.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU.  The opposite of the bin.seqs command.

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

 </help>
</tool>