annotate taxonomy_krona_chart.xml @ 0:bd565e1e3c5f draft

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<tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.4">kronatools</requirement>
  </requirements>
  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
  <command>
    #if $input.ext == 'taxonomy'
      ktImportGalaxy "${input}" -o "${output}"
    #else
      ktImportText "${input}" -o "${output}"
    #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" />
  </inputs>
  <outputs>
    <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
  </outputs>
  <help>
**What it does**

This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_.
It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools.

.. _Krona: http://sourceforge.net/p/krona/home/krona/

------

**License and citation**

This Galaxy tool is Copyright © 2013-2014 `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 |Cuccuru2014|_.

.. |Cuccuru2014| 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
.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135

This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_.

.. _Krona: http://sourceforge.net/p/krona/home/krona/
.. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385
.. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385
  </help>
</tool>