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1 <tool id="conifer_plotcalls" name="CoNIFER plot caller" version="1.0">
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2 <description>cnv caller</description>
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3 <command interpreter="perl">
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4 conifer_wrapper.pl --input $input --regions $plot_option.regions --html_file $html_file --html_folder $html_file.files_path
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5 #if str($plot_option.plot_option_select) == "single"
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6 --sample "$plot_option.sample"
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7 #else
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8 --window $plot_option.window
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9 --multiple
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10 #end if
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11 2>&1
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12 </command>
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13 <inputs>
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14 <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (hdf5)"/>
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15 <conditional name="plot_option">
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16 <param name="plot_option_select" type="select" label="Single or multiple regions?">
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17 <option value="single" selected="true">Single region</option>
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18 <option value="multiple">Multiple regions</option>
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19 </param>
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20 <when value="single">
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21 <param name="regions" type="text" size="50" optional="false" label="Region" help="Region for the plot (i.e. chr1:1000-2000)"/>
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22 <param name="sample" type="text" size="50" optional="true" value="" label="Sample" help="Sample names to be highlighted in the plot (optional)"/>
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23 </when>
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24 <when value="multiple">
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25 <param format="tabular" name="regions" type="data" label="CoNIFER output calls file (tabular)"/>
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26 <param name="window" size="10" type="integer" value="50" label="Window"/>
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27 </when>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data format="html" name="html_file" label="${tool.name} on ${on_string}" />
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32 </outputs>
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33 <help>
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34 **What it does**
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35
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36 Draw a HTML page with CNV plots. It accepts as input either a single region or a file with CoNIFER calls.
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37
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38 **License and citation**
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39
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40 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
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41
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42 .. _CRS4 Srl.: http://www.crs4.it/
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43 .. _MIT license: http://opensource.org/licenses/MIT
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44
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45 If you use this tool in Galaxy, please cite |Cuccuru2014|_.
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46
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47 .. |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
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48 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135
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49
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50 This tool uses CoNIFER, which is licensed separately. Please cite:
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51
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52 - |Krumm2012|_.
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53
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54 .. |Krumm2012| replace:: (Krumm et al., 2012) Copy number variation detection and genotyping from exome sequence data. Genome research.
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55 .. _Krumm2012: http://genome.cshlp.org/content/22/8/1525.full?sid=4a7a300a-b960-4544-8611-effc3315411c
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56 </help>
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57 </tool>
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