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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="get_gb_sp" name="Get_GB_sp" version="1.0">
2 <description> Grab All GenBank Data from a text list of species </description>
3 <requirements>
4 <requirement type="perl-module">Bio</requirement>
5 </requirements>
6 <command interpreter="perl">
7 get_gb_sp.pl $data_file $database $outtype $outfile $nffile 2> error.log
8 </command>
9 <inputs>
10 <param format="txt" name="data_file" type="data" optional="false" label="Text list of species" help="One species per line"/>
11
12 <param name="database" type="select" label="Protein or Nucleotide Data">
13 <option value="nucleotide">Nucleotide</option>
14 <option value="protein">Protein</option>
15 </param>
16
17 <param name="outtype" type="select" label="Output File Format">
18 <option value="fasta">Fasta</option>
19 <option value="genbank">GenBank</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data format="txt" name="nffile" label="No genbank data ${tool.name} with ${on_string}" />
24 <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" />
25 </outputs>
26 <help>
27 **What it does**
28
29 Downloads ALL data from GenBank based on species names.
30
31 ------
32
33 **Inputs**
34
35 A text list of species names (or genus names will retrieve all data for a genus.)
36
37 ------
38
39 **Outputs**
40
41 The user selects which output format to use for data downloaded from GenBank. Options Include::
42 1. GenBank format
43 2. FASTA format
44
45 -------
46
47 **Additional Information**
48
49 GenBank format can be converted to phytab or other formats using GenBankstrip.
50
51 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
52
53 -------
54
55 **Citations**
56
57 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.
58
59 Current Osiris Citation is here
60
61 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
62
63 </help>
64 </tool>