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