|
7
|
1 <tool id="conifer_call" name="CoNIFER CNVs caller" version="1.0">
|
|
|
2 <description></description>
|
|
13
|
3 <command>
|
|
30
|
4 python $__tool_directory__/conifer.py call
|
|
7
|
5 --input $input
|
|
|
6 --output temporary
|
|
|
7 --threshold $threshold
|
|
|
8 2>&1
|
|
|
9 && awk '{print \$2,\$3,\$4,\$5,\$1}' OFS="\t" temporary > $outputFile
|
|
|
10 </command>
|
|
|
11 <inputs>
|
|
|
12 <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (HDF5)" />
|
|
|
13 <param name="threshold" type="float" value="1.5" label="Threshold" />
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <data format="bed" name="outputFile" label="${tool.name} on ${on_string}" />
|
|
|
17 </outputs>
|
|
|
18 <help>
|
|
|
19 **What it does**
|
|
|
20
|
|
|
21 This tool is a CNVs caller using SVD-ZRPKM thresholding.
|
|
|
22
|
|
|
23 **License and citation**
|
|
|
24
|
|
|
25 This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
|
|
|
26
|
|
|
27 .. _CRS4 Srl.: http://www.crs4.it/
|
|
|
28 .. _MIT license: http://opensource.org/licenses/MIT
|
|
|
29
|
|
|
30 You can use this tool only if you agree to the license terms of: `CoNIFER`_.
|
|
|
31
|
|
|
32 .. _CoNIFER: http://conifer.sourceforge.net/
|
|
|
33
|
|
|
34 If you use this tool, please cite:
|
|
|
35
|
|
|
36 - |Cuccuru2014|_
|
|
|
37 - |Krumm2012|_.
|
|
|
38
|
|
|
39 .. |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
|
|
|
40 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
|
|
|
41 .. |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
|
|
|
42 .. _Krumm2012: http://genome.cshlp.org/content/22/8/1525
|
|
|
43 </help>
|
|
|
44 <citations>
|
|
|
45 <citation type="doi">10.1093/bioinformatics/btu135</citation>
|
|
|
46 <citation type="doi">10.1101/gr.138115.112</citation>
|
|
|
47 </citations>
|
|
|
48 </tool>
|
