--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_phylogeny.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,75 @@
+<tool id="qiime_make_phylogeny" name="Make phylogeny" version="1.9.1">
+
+    <description></description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        make_phylogeny.py --version
+    ]]>
+    </version_command>
+
+    <stdio></stdio>
+
+    <command>
+<![CDATA[  
+        make_phylogeny.py 
+            -i $input_fp
+            -o $result_fp
+            -t $tree_method
+            -l $log_fp
+            -r $root_method
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="input_fp" type="data" format="fasta" 
+            label="Input fasta alignment" help="(-i/--input_fp)"/>
+
+        <param name="tree_method" type="select" 
+            label="Method for tree building" help="(-t/--tree_method)">
+            <option value="clustalw">ClustalW</option>
+            <option value="raxml_v730">raxml_v730</option>
+            <option value="muscle">muscle</option>
+            <option value="fasttree" selected="true">fasttree</option>
+            <option value="clearcut">clearcut</option>
+        </param>
+
+        <param name="root_method" type="select" 
+            label="Method for choosing root of phylo tree" help="(-r/--root_method)">
+            <option value="midpoint">Midpoint</option>
+            <option value="tree_method_default" selected="true">Default method of tree method</option>
+        </param>
+
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="result_fp" 
+            label="${tool.name} on ${on_string}: Tree"/>
+        <data format="txt" name="log_fp" 
+            label="${tool.name} on ${on_string}: Log"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>