--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/make_phylogeny.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,49 @@
+<tool id="make_phylogeny" name="make_phylogeny" version="2.0.0">
+ <description>Make Phylogeny</description>
+ <requirements>
+  <requirement type="binary">make_phylogeny.py</requirement>
+ </requirements>
+ <command interpreter="python">
+ qiime_wrapper.py
+ --galaxy_inputdir='$__new_file_path__'
+ --galaxy_ext_change='$input_fp'
+ --galaxy_new_ext='fasta'
+ make_phylogeny.py
+ --input_fp='$__new_file_path__'/temporary.fasta
+ --tree_method=$tree_method
+ --result_fp=$result_fp
+ --log_fp=$log_fp
+ --root_method=$root_method</command>
+ <inputs>
+  <param name="input_fp" type="data" format="align" label="input_fp"
+   help="Path to read input alignment (output from filter_alignment) [REQUIRED]"/>
+  <param name="tree_method" type="select" label="tree_method"
+   help="Method for tree building. [default: fasttree]">
+    <option value="clearcut">clearcut</option>
+    <option value="clustalw">clustalw</option>
+    <option value="raxml">raxml</option>
+    <option value="fasttree_v1">fasttree_v1</option>
+    <option value="fasttree" selected="true">fasttree</option>
+    <option value="muscle">muscle</option>
+  </param>
+  <param name="root_method" type="select" label="root_method"
+   help="method for choosing root of phylo tree [default: tree_method_default]">
+    <option value="tree_method_default" selected="true">tree_method_default</option>
+    <option value="midpoint">midpoint</option>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
+  <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>For more information, see make_phylogeny_ 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
+
+.. _make_phylogeny: http://qiime.org/scripts/make_phylogeny.html</help>
+</tool>
+