--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/principal_coordinates.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,40 @@
+<tool id="principal_coordinates" name="principal_coordinates" version="1.2.0">
+ <description>Principal Coordinates Analysis (PCoA)</description>
+ <requirements>
+  <requirement type="binary">principal_coordinates.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  principal_coordinates.py
+  --input_path=$input_path
+  --output_path=$output_path
+ </command>
+ <inputs>
+ <conditional name="run_type">
+  <param name="input_type" type="select" label="Input Type" help="Select the type/number of input file(s). If you want to process multiple diversity metrics, select 'multiple files.'">
+   <option value="single">Single File</option>
+   <option value="multi">Multiple Files</option>
+  </param>
+  <when value="single">
+   <param name="input_path" type="data" format="qiimedistmat"  label="input_path"
+   help="path to the input distance matrix file (i.e., the output from beta_diversity.py). [REQUIRED]"/>
+  </when>
+  <when value="multi">
+    <param name="input_path" type="data" format="qiimedistmat"  label="input_path"
+   help="Path to the first distance matrix file of the metrics run. Example: if you ran beta diversity for both 1: unweighted and 2: weighted unifrac, choose the unweighted file. [REQUIRED]"/>
+  </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="qiimepca" name="output_path" label="${tool.name} on ${on_string}: coordinates"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>For more information, see principle_coordinates_ in the Qiime documentation.
+ 
+Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
+Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
+ 
+ .. _principle_coordinates: http://qiime.org/scripts/principal_coordinates.html</help>
+</tool>
+