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comparison get_fasta_from_taxon.xml @ 0:7ce8da107910 draft default tip

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author crs4
date Wed, 11 Sep 2013 06:07:50 -0400
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1 <tool id="get_fasta_from_taxon" name="Get FASTA from taxon" version="1.0.1">
2 <description></description>
3 <command interpreter="python">get_fasta_from_taxon.py -i $taxid -d $dbname -o $outfilename -l $logfile </command>
4
5 <inputs>
6 <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" />
7 <param name="dbname" type="select" label="NCBI database">
8 <option value="nuccore">Nucleotide</option>
9 <option value="protein">Protein</option>
10 </param>
11 </inputs>
12 <outputs>
13 <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: taxid${taxid.value}.${dbname.value_label}.fasta" />
14 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
15 </outputs>
16 <tests>
17
18 </tests>
19 <help>
20 **What it does**
21
22 This tool retrieves all nucleotidic/peptidic sequences from the corresponding NCBI database for a given taxonomy ID.
23
24 **License and citation**
25
26 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
27
28 .. _CRS4 Srl.: http://www.crs4.it/
29 .. _MIT license: http://opensource.org/licenses/MIT
30
31 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
32
33 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
34 .. _Cuccuru2013: http://orione.crs4.it/
35 </help>
36 </tool>