<tool id="anomaly_wrapper" name="Anomaly" version="0.2">
  <description></description>
  <requirements>
    <requirement type="package" version="3.02">glimmer</requirement>
  </requirements>
  <command interpreter="python">
    anomaly_wrapper.py --anSequence $anSequence --anCoords $anCoords
    #if $anStartCodons
      --anStartCodons="$anStartCodons"
    #end if
    #if $anCheckFirstCodon
      --anCheckFirstCodon
    #end if
    #if $anCheckStopCodon
      --anCheckStopCodon
    #end if
    #if $anStopCodons
      --anStopCodons="$anStopCodons"
    #end if
    --anOutput $anOutput --logfile $logfile
 </command>

  <inputs>
    <param name="anSequence" type="data" format="fasta" label="DNA sequence to be analyzed" help="FASTA format" />

    <param name="anCoords" type="data" format="glimmer_coords" label="Region coordinates" />

    <param name="anStartCodons" type="text" value="" optional="true" label="Specify allowable start codons as a comma-separated list (-A)" help="Sample format: 'atg,gtg' . The default start codons are atg, gtg and ttg." />

    <param name="anCheckFirstCodon" type="boolean" checked="false" label="Omit the check that the first codon is a start codon (-s)" help="" />

    <param name="anCheckStopCodon" type="boolean" checked="false" label="Check whether the codon preceding the start coordinate position is a stop codon (-t)" help="This is useful if the coordinates represent the entire region between stop codons." />

    <param name="anStopCodons" type="text" value="" optional="true" label="Specify allowable stop codons as a comma-separated list (-Z)" help="Sample format: 'tag,tga'. The default stop codons are tag, tga and taa." />
  </inputs>

  <outputs>
    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
    <data name="anOutput" format="txt" label="${tool.name} on ${on_string}: output" />
  </outputs>

  <tests>

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

Read DNA sequence in "sequence-file" and for each region specified by the coordinates in "coord-file", check whether the region represents a normal gene, i.e., it begins with a start codon, ends with a stop codon, and has no frame shifts.

**License and citation**

This Galaxy tool is Copyright © 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/

This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.

.. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
.. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
.. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
  </help>
</tool>