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<tool id="conifer_plotcalls" name="CoNIFER plot caller" version="1.0">
	<description>cnv caller</description>
	<command interpreter="perl">
    conifer_wrapper.pl --input $input --regions $plot_option.regions --html_file $html_file --html_folder $html_file.files_path
    #if str($plot_option.plot_option_select) == "single"
        --sample "$plot_option.sample"
    #else
        --window $plot_option.window
        --multiple
    #end if
    2&gt;&amp;1
	</command>
	<inputs>
		<param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (hdf5)"/>
		<conditional name="plot_option">
			<param name="plot_option_select" type="select" label="Single or multiple regions?">
				<option value="single" selected="true">Single region</option>
				<option value="multiple">Multiple regions</option>
			</param>
			<when value="single">
				<param name="regions" type="text" size="50" optional="false" label="Region" help="Region for the plot (i.e. chr1:1000-2000)"/>
				<param name="sample" type="text" size="50" optional="true" value="" label="Sample" help="Sample names to be highlighted in the plot (optional)"/>
			</when>
			<when value="multiple">
				<param format="tabular" name="regions" type="data" label="CoNIFER output calls file (tabular)"/>
                <param name="window" size="10" type="integer" value="50" label="Window"/>
			</when>
		</conditional>
    </inputs>
    <outputs>
        <data format="html" name="html_file" label="${tool.name} on ${on_string}" />
    </outputs>
<help>
**What it does**

Draw a HTML page with CNV plots. It accepts as input either a single region or a file with CoNIFER calls.

**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 |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/2014/03/10/bioinformatics.btu135

This tool uses CoNIFER, which is licensed separately. Please cite:

- |Krumm2012|_.

.. |Krumm2012| replace::  (Krumm et al., 2012) Copy number variation detection and genotyping from exome sequence data. Genome research.
.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525.full?sid=4a7a300a-b960-4544-8611-effc3315411c
  </help>
</tool>