--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/pick_rep_set.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,53 @@
+<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>
+