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<tool id="conifer_call" name="CoNIFER CNVs caller" version="1.0">
  <description></description>
  <command>
       python $__tool_directory__/conifer.py call
	--input $input
	--output temporary
    --threshold $threshold
	2&gt;&amp;1
    &amp;&amp; awk '{print \$2,\$3,\$4,\$5,\$1}' OFS="\t" temporary &gt; $outputFile
  </command>
  <inputs>
    <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (HDF5)" />
    <param name="threshold" type="float" value="1.5" label="Threshold" />
  </inputs>
  <outputs>
    <data format="bed" name="outputFile" label="${tool.name} on ${on_string}" />
  </outputs>
 <help>
**What it does**

This tool is a CNVs caller using SVD-ZRPKM thresholding.

**License and citation**

This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.

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

You can use this tool only if you agree to the license terms of: `CoNIFER`_.

.. _CoNIFER: http://conifer.sourceforge.net/

If you use this tool, please cite:

- |Cuccuru2014|_
- |Krumm2012|_.

.. |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* 30(13), 1928-1929
.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
.. |Krumm2012| replace::  Krumm, N., Sudmant, P. H., Ko, A., O'Roak, B. J., Malig, M., Coe, B. P., NHLBI Exome Sequencing Project, Quinlan, A. R., Nickerson, D. A., Eichler, E. E. (2012) Copy number variation detection and genotyping from exome sequence data. *Genome Res.* 22(8), 1525-1532
.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu135</citation>
    <citation type="doi">10.1101/gr.138115.112</citation>
  </citations>
</tool>