<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>