--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_phylogeny.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,43 @@
+<tool id="make_phylogeny" name="make_phylogeny" version="1.2.0">
+ <description>Make Phylogeny</description>
+ <requirements>
+  <requirement type="binary">make_phylogeny.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  make_phylogeny.py
+  --input_fp=$input_fp
+  --tree_method=$tree_method
+  --root_method=$root_method
+  --result_fp=$result_fp
+  --log_fp=$log_fp
+ </command>
+ <inputs>
+  <param name="input_fp" type="data" format="align" label="input_fp"
+   help="Path to read input alignment [REQUIRED]"/>
+  <param name="tree_method" type="select" label="tree_method"
+   help="Method for tree building. Valid choices are: clearcut, clustalw, raxml, fasttree_v1, fasttree, muscle [default: fasttree]">
+    <option value="clearcut">clearcut</option>
+    <option value="clustalw">clustalw</option>
+    <option value="raxml">raxml</option>
+    <option value="fasttree_v1">fasttree_v1</option>
+    <option value="fasttree" selected="true">fasttree</option>
+    <option value="muscle">muscle</option>
+  </param>
+  <param name="root_method" type="select" label="root_method"
+   help="method for choosing root of phylo tree  Valid choices are: midpoint, tree_method_default [default: tree_method_default]">
+    <option value="tree_method_default" selected="true">tree_method_default</option>
+    <option value="midpoint">midpoint</option>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
+  <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+