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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="generate_from_phylota" name="Generate_from_PhyLoTA" version="1.0">
2 <description>Pull phylogenies and genetic data from phylota with species list input</description>
3 <requirements>
4 <requirement type="perl-module">Bio</requirement>
5 <requirement type="perl-module">LWP</requirement>
6 </requirements>
7 <command interpreter="perl">
8 generate_from_phylota.pl $infile $database $outfile $treefile $phytabfile
9 </command>
10 <inputs>
11 <param name="infile" type="data" format="txt" label="Input File" help="text list of species to download data from" />
12 <param name="database" type="data" format="txt" label="Phylota tree list" help="List available here: http://phylota.net/pb/Download/pb.dmp.maximalnr.trees.184.gz" />
13 </inputs>
14 <outputs>
15 <data format="fasta" name="outfile" label="fasta file from ${tool.name} on ${on_string}: Out file" />
16 <data format="newick" name="treefile" label="Trees from ${tool.name} on ${on_string}: Out file" />
17 <data format="tabular" name="phytabfile" label="phytab from ${tool.name} on ${on_string}: Out file" />
18 </outputs>
19 <help>
20 **What it does**
21
22 Generate_from_PhyLoTA pulls pre-calculated trees and corresponding raw data from the PhyLoTA browser. The PhyLoTA browser groups
23 GenBank data into gene clusters by similarity, and uses those clusters for phylogenetic analysis.
24
25 ------
26
27 **Inputs**
28
29 1. A target list of species.
30 2. The pre-calculated set of phylota trees available from the phylota web page. Available here: http://phylota.net/pb/Download/pb.dmp.maximalnr.trees.184.gz
31
32 ------
33
34 **Outputs**
35
36 1. All raw sequence data in fasta format for the trees in #2.
37 2. All trees in newick format. Trees will contain more species than the species list, and all species are retained.
38 3. All raw sequence data in PHYTAB format. http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
39
40 -------
41
42 **Additional Information**
43
44 http://osiris-phylogenetics.blogspot.com/2012/09/generatefromphylota.html
45
46 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
47
48 -------
49
50 **Citations**
51
52 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.
53
54 Current Osiris Citation is here
55
56 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
57
58 Additional Citations for this tool
59
60 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.
61
62 </help>
63 </tool>
64
65