<tool id="get_fasta_from_taxon" name="Get FASTA from taxon" version="1.0.1">
  <description></description>
  <command interpreter="python">get_fasta_from_taxon.py -i $taxid -d $dbname -o $outfilename -l $logfile </command>

  <inputs>
    <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" />
    <param name="dbname" type="select" label="NCBI database">
      <option value="nuccore">Nucleotide</option>
      <option value="protein">Protein</option>
    </param>
  </inputs>
  <outputs>
    <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: taxid${taxid.value}.${dbname.value_label}.fasta" />
    <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  <tests>

  </tests>
  <help>
**What it does**

This tool retrieves all nucleotidic/peptidic sequences from the corresponding NCBI database for a given taxonomy ID.

**License and citation**

This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

If you use this tool in Galaxy, please cite |Cuccuru2013|_.

.. |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*
.. _Cuccuru2013: http://orione.crs4.it/
  </help>
</tool>