annotate get_edge_data.xml @ 2:bad8a51514dd draft

Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.

<tool id="get_edge_data" name="Get EDGE-pro files" version="1.0.1">
  <description></description>
  <command interpreter="python">get_edge_data.py -i "$gbkid" --fna $fnafile --ptt $pttfile --rnt $rntfile --gff $gfffile</command>

  <inputs>
    <param name="gbkid" type="text" value="NC_" label="RefSeq Genomic Accession ID">
      <validator type="empty_field" />
    </param>
  </inputs>
  <outputs>
    <data name="fnafile" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
    <data name="pttfile" format="ptt" label="${tool.name} on ${on_string}: PTT" />
    <data name="rntfile" format="rnt" label="${tool.name} on ${on_string}: RNT" />
    <data name="gfffile" format="gff" label="${tool.name} on ${on_string}: GFF" />
  </outputs>
  <tests>

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

This tool retrieves from NCBI the files required by `EDGE-pro`_.

.. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/

**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. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
.. _Cuccuru2013: http://orione.crs4.it/
  </help>
</tool>