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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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1 <tool id="phylota_with_taxid" name="PhyLoTA_with_taxID" version="1.0">
2 <description>Pull all genetic data from phylota using a GenBank Taxonomy ID</description>
3 <requirements>
4 <requirement type="perl-module">Bio</requirement>
5 <requirement type="perl-module">LWP</requirement>
6 </requirements>
7 <command interpreter="perl">
8 phylota_with_taxid.pl $input $outfile $phytabfile
9 </command>
10 <inputs>
11 <param name="input" type="integer" value="0" label="Taxon ID" help="GenBank TaxonID" />
12 </inputs>
13 <outputs>
14 <data format="fasta" name="outfile" label="fasta file from ${tool.name} on ${on_string}: Out file" />
15 <data format="tabular" name="phytabfile" label="phytab from ${tool.name} on ${on_string}: Out file" />
16 </outputs>
17 <help>
18 **What it does**
19
20 PhyLoTA_with_taxID pulls pre-calculated trees and corresponding raw data from the PhyLoTA browser. The PhyLoTA browser groups GenBank
21 data into gene clusters by similarity, and uses those clusters for phylogenetic analysis.
22
23 ------
24
25 **Inputs**
26
27 1. A GenBank Taxon ID.
28 Search Here for ID of a taxon
29 http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
30
31 ------
32
33 **Outputs**
34
35 1. All raw sequence data in fasta format for the trees in #2.
36 2. All raw sequence data in PHYTAB format. http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
37
38 -------
39
40 **Additional Information**
41
42 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
43
44 ------
45
46 **Citations**
47
48 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.
49
50 Current Osiris Citation is here
51
52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
53
54 Additional Citations for this tool
55
56 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.
57
58 </help>
59 </tool>
60
61