--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_diversity.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,61 @@
+<tool id="alpha_diversity" name="alpha_diversity" version="1.2.0">
+ <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description>
+ <requirements>
+  <requirement type="binary">alpha_diversity.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  alpha_diversity.py
+  --input_path=$input_path
+  --output_path=$output_path
+  --metrics=$metrics
+  #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
+    --tree_path=$tree_path
+  #end if
+
+ </command>
+ <inputs>
+  <param name="input_path" type="data"  format="tabular"  label="OTU table"
+   help="input path.  directory for batch processing, filename for single file operation"/>
+  <param name="metrics" type="select"  multiple="true" label="metrics"
+   help="metrics to use">
+      <option value="ACE">ACE</option>
+      <option value="berger_parker_d">berger_parker_d</option>
+      <option value="brillouin_d">brillouin_d</option>
+      <option value="chao1">chao1</option>
+      <option value="chao1_confidence">chao1_confidence</option>
+      <option value="dominance">dominance</option>
+      <option value="doubles">doubles</option>
+      <option value="equitability">equitability</option>
+      <option value="fisher_alpha">fisher_alpha</option>
+      <option value="heip_e">heip_e</option>
+      <option value="kempton_taylor_q">kempton_taylor_q</option>
+      <option value="margalef">margalef</option>
+      <option value="mcintosh_d">mcintosh_d</option>
+      <option value="mcintosh_e">mcintosh_e</option>
+      <option value="menhinick">menhinick</option>
+      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
+      <option value="observed_species">observed_species</option>
+      <option value="osd">osd</option>
+      <option value="reciprocal_simpson">reciprocal_simpson</option>
+      <option value="robbins">robbins</option>
+      <option value="shannon">shannon</option>
+      <option value="simpson">simpson</option>
+      <option value="simpson_e">simpson_e</option>
+      <option value="singles">singles</option>
+      <option value="strong">strong</option>
+      <option value="PD_whole_tree">PD_whole_tree</option>
+  </param>
+  <param name="tree_path" type="data"  format="tre"  label="tree_path" optional="true"
+   help="path to newick tree file, required for phylogenetic metrics: PD_whole_tree"/>
+ </inputs>
+ <outputs>
+  <data format="tabular" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+