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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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<tool id="phylota_with_taxid" name="PhyLoTA_with_taxID" version="1.0">
    <description>Pull all genetic data from phylota using a GenBank Taxonomy ID</description>
    <requirements>
	<requirement type="perl-module">Bio</requirement>
	<requirement type="perl-module">LWP</requirement>
    </requirements>		
    <command interpreter="perl">
		phylota_with_taxid.pl $input $outfile $phytabfile
    </command>
    <inputs>
	    <param name="input" type="integer" value="0" label="Taxon ID" help="GenBank TaxonID" />
    </inputs>
    <outputs>
	<data format="fasta" name="outfile" label="fasta file from ${tool.name} on ${on_string}: Out file" />
	<data format="tabular" name="phytabfile" label="phytab from ${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>
**What it does**

PhyLoTA_with_taxID pulls pre-calculated trees and corresponding raw data from the PhyLoTA browser. The PhyLoTA browser groups GenBank 
data into gene clusters by similarity, and uses those clusters for phylogenetic analysis.

------

**Inputs**

1. A GenBank Taxon ID.
Search Here for ID of a taxon
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

------

**Outputs**

1. All raw sequence data in fasta format for the trees in #2.
2. All raw sequence data in PHYTAB format. http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

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**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

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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

Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. 2008. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Syst. Biol. 57:335-346. 

    </help>
</tool>