--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylomatic/phylomatic.xml	Thu Jun 21 17:46:55 2012 -0400
@@ -0,0 +1,29 @@
+<tool id="phylomatic" name="Phylomatic">
+	<description>Run Phylomatic</description>
+	<command interpreter="perl">./phylomatic.pl $input1 $input2</command>
+	<inputs>
+		<param name="input1" type="data" format="txt" label="Phylogenetic Tree" />
+		<param name="input2" type="data" format="txt" label="Taxonomy File" />
+	</inputs>
+
+	<outputs>
+		<data from_work_dir="output.txt"/>
+	</outputs>
+	
+	<help>
+	Phylomatic (Part of Phylocom)
+	
+	http://www.phylodiversity.net/phylomatic/phylomatic.html
+	
+	The online software takes your list of taxa, and first tries to match them by genus name to the megatree. 
+	Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. 
+	If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. 
+	Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
+	(http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
+	
+	http://bioinformatics.oxfordjournals.org/content/24/18/2098
+	Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100.
+
+	</help>
+</tool>
+