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comparison getdata/generate_from_phylota.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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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 |