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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_1_gb" name="Get_1_GB" version="1.0">
2 <description> Grab one sequence from GenBank using accession number query </description>
3 <requirements>
4 <requirement type="package">bioperl</requirement>
5 </requirements>
6 <command interpreter="perl">
7 get_1_gb.pl $acc $database $outtype $outfile 2>&amp;1
8 </command>
9 <inputs>
10 <param name="acc" type="text" label="Accession Number" />
11 <param name="database" type="select" label="Protein or Nucleotide Data">
12 <option value="nucleotide">Nucleotide</option>
13 <option value="protein">Protein</option>
14 </param>
15 <param name="outtype" type="select" label="File Format">
16 <option value="fasta">Fasta</option>
17 <option value="genbank">GenBank</option>
18 </param>
19 </inputs>
20 <outputs>
21 <data format="txt" name="outfile" label="Sequence data from ${tool.name} with ${on_string}" />
22 </outputs>
23 <help>
24 **What it does**
25
26 Get_1_GB grabs one sequence from GenBank using accession number query.
27
28 ------
29
30 **Inputs**
31
32 GenBank accession number
33
34 ------
35
36 **Outputs**
37
38 FASTA or GenBank
39
40 -------
41
42 **Additional Information**
43
44 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
45
46 -------
47
48 **Citations**
49
50 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.
51
52 Current Osiris Citation is here
53
54 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
55
56 Additional Citations for this tool
57
58 Link to Genbank: http://www.ncbi.nlm.nih.gov/genbank/
59 </help>
60 </tool>