--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pick_rep_set.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,64 @@
+<tool id="qiime_pick_rep_set" name="pick rep set" version="1.9.1galaxy1">
+    <description>Pick representative set of sequences</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command>
+<![CDATA[
+        pick_rep_set.py 
+            -i $input_file
+            -m $rep_set_picking_method
+            -s $sort_by
+            #if str($fasta_file) != 'None':
+             -f $fasta_file
+            #end if
+             -o $result_fp -l rep_set.log
+
+            #if str($reference_seqs_fp) != 'None':
+             -r $reference_seqs_fp
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param label="-i/--input_file: Path to input otu mapping file [REQUIRED]" name="input_file" optional="False" type="data"/>
+        <param label="-f/--fasta_file: Path to input fasta file [REQUIRED if not picking against a reference set; default: None]" name="fasta_file" optional="True" type="data"/>
+        <param label="-m/--rep_set_picking_method: Method for picking representative sets.  Valid choices are random, longest, most_abundant, first [default: first (first chooses cluster seed when picking otus with uclust)]" name="rep_set_picking_method" optional="True" type="select">
+            <option value="random">random</option>
+            <option value="longest">longest</option>
+            <option value="most_abundant">most_abundant</option>
+            <option value="first">first</option>
+        </param>
+        <param label="-s/--sort_by: sort by otu or seq_id [default: otu]" name="sort_by" optional="True" type="select">
+            <option value="otu">otu</option>
+            <option value="seq_id">seq_id</option>
+        </param>
+        <param label="-r/--reference_seqs_fp: collection of preferred representative sequences [default: None]" name="reference_seqs_fp" optional="True" type="data"/>
+    </inputs>
+
+    <outputs>
+        <data format="fasta" name="result_fp" label="rep_set_seqs.fasta"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**How it does?**
+
+After picking OTUs, you can then pick a representative set of sequences. For each OTU, you will end up with one sequence that can be used in subsequent analyses.
+
+The output from pick_rep_set.py is a single FASTA file containing one sequence per OTU. The FASTA header lines will be the OTU identifier (from here on used as the unique sequence identifier) followed by a space, followed by the sequence identifier originally associated with the representative sequence. The name of the output FASTA file will be <input_sequences_filepath>_rep_set.fasta by default, or can be specified via the "-o" parameter.
+]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>