<tool id="pick_rep_set" name="pick_rep_set" version="2.0.0">
 <description>Pick representative set of sequences</description>
 <requirements>
  <requirement type="binary">pick_rep_set.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  pick_rep_set.py
  --input_file=$input_file
  #if $reference_seqs_fp.__str__ != 'None' or $reference_seqs_fp != None and $reference_seqs_fp.__str__ == '':
  --reference_seqs_fp=$reference_seqs_fp
  #else:
  --fasta_file=$fasta_file
  #end if
  --rep_set_picking_method=$rep_set_picking_method
  --sort_by=$sort_by
  --log_fp=$log_fp
  --result_fp=$result_fp
 </command>
 <inputs>
  <param name="input_file" type="data" format="qiimeotu" label="input_file"
   help="Path to input otu mapping file (usually output from pick_otus) [REQUIRED]"/>
  <param name="fasta_file" type="data" format="fasta" optional="true" label="fasta_file"
   help="Path to input fasta file [REQUIRED if not picking against a reference set; default: None]"/>
  <param name="rep_set_picking_method" type="select" label="rep_set_picking_method"
   help="Method for picking representative sets. [default: first]">
    <option value="random">random</option>
    <option value="longest">longest</option>
    <option value="most_abundant">most_abundant</option>
    <option value="first" selected="true">first</option>
  </param>
  <param name="sort_by" type="select" value="otu" label="sort_by" >
    <option value="otu" selected="true">otu</option>
    <option value="seq_id">seq_id</option>
  </param>
  <param name="reference_seqs_fp" type="data" format="fasta" optional="true" label="reference_seqs_fp"
   help="collection of preferred representative sequences"/>
 </inputs>
 <outputs>
   <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
   <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: rep_set.fasta" />
 </outputs>
 <tests>
 </tests>
 <help>For more information, see pick_rep_set_ in the Qiime documentation.
   
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _pick_rep_set: http://qiime.org/scripts/pick_rep_set.html</help>
</tool>