<tool id="phylomatic" name="Phylomatic" version="1.0.1">
	<description>Run Phylomatic</description>
	<requirements>
		<requirement type="binary">Phylocom Phylomatic</requirement>
	</requirements>
	<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>
**What it does**

Phylomatic (Webb & Donoghue, 2005) is part of the Phylocom software package (Webb et al., 2008).
Phylomatic 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.

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**Inputs**

Input 1: Phylogeny in Newick format.
Input 2: List of taxa in delimited text file. 

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**Outputs**

Phylomatic matches input taxa to the most resolved possible position in any of a set of master 
trees in the database (the 'megatrees') and returns the phylogeny in one of a variety of formats: 
graphical, Newick, NEXUS, or tabular.

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**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use 
of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

Phylomatic (Part of Phylocom software package)

http://phylodiversity.net/phylomatic/html/pm2_form.html

If you use results derived from Phylocom analyses in your publications, please cite:

Webb, C. O., Ackerly, D. D. & Kembel, S. W. 2008. Phylocom: software for the analyses of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2089-2100. 
doi: 10.1093/bioinformatics/btn358

Original Phylomatic citation:

Webb, C. O. & Donoghue, M. J. 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular 
Ecology Resources, 5: 181-183. doi: 10.1111/j.1471-8286.2004.00829.x
	</help>
</tool>