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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_fasta_from_taxon.xml	Wed Sep 11 06:07:50 2013 -0400
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+<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>