Mercurial > repos > bzonnedda > conifer
comparison conifer/c_plotcalls.xml @ 0:ca5354286bee draft
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author | bzonnedda |
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date | Tue, 18 Oct 2016 09:26:52 -0400 |
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1 <tool id="conifer_plotcalls" name="CoNIFER plot caller" version="1.0"> | |
2 <description>cnv caller</description> | |
3 <command interpreter="perl"> | |
4 conifer_wrapper.pl --input $input --regions $plot_option.regions --html_file $html_file --html_folder $html_file.files_path | |
5 #if str($plot_option.plot_option_select) == "single" | |
6 --sample "$plot_option.sample" | |
7 #else | |
8 --window $plot_option.window | |
9 --multiple | |
10 #end if | |
11 2>&1 | |
12 </command> | |
13 <inputs> | |
14 <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (hdf5)"/> | |
15 <conditional name="plot_option"> | |
16 <param name="plot_option_select" type="select" label="Single or multiple regions?"> | |
17 <option value="single" selected="true">Single region</option> | |
18 <option value="multiple">Multiple regions</option> | |
19 </param> | |
20 <when value="single"> | |
21 <param name="regions" type="text" size="50" optional="false" label="Region" help="Region for the plot (i.e. chr1:1000-2000)"/> | |
22 <param name="sample" type="text" size="50" optional="true" value="" label="Sample" help="Sample names to be highlighted in the plot (optional)"/> | |
23 </when> | |
24 <when value="multiple"> | |
25 <param format="tabular" name="regions" type="data" label="CoNIFER output calls file (tabular)"/> | |
26 <param name="window" size="10" type="integer" value="50" label="Window"/> | |
27 </when> | |
28 </conditional> | |
29 </inputs> | |
30 <outputs> | |
31 <data format="html" name="html_file" label="${tool.name} on ${on_string}" /> | |
32 </outputs> | |
33 <help> | |
34 **What it does** | |
35 | |
36 Draw a HTML page with CNV plots. It accepts as input either a single region or a file with CoNIFER calls. | |
37 | |
38 **License and citation** | |
39 | |
40 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. | |
41 | |
42 .. _CRS4 Srl.: http://www.crs4.it/ | |
43 .. _MIT license: http://opensource.org/licenses/MIT | |
44 | |
45 If you use this tool in Galaxy, please cite |Cuccuru2014|_. | |
46 | |
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 | |
48 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135 | |
49 | |
50 This tool uses CoNIFER, which is licensed separately. Please cite: | |
51 | |
52 - |Krumm2012|_. | |
53 | |
54 .. |Krumm2012| replace:: (Krumm et al., 2012) Copy number variation detection and genotyping from exome sequence data. Genome research. | |
55 .. _Krumm2012: http://genome.cshlp.org/content/22/8/1525.full?sid=4a7a300a-b960-4544-8611-effc3315411c | |
56 </help> | |
57 </tool> |