Mercurial > repos > bzonnedda > conifer
changeset 4:59fb4f2931df draft
Deleted selected files
| author | bzonnedda |
|---|---|
| date | Mon, 20 Feb 2017 06:24:13 -0500 |
| parents | 28d28bc2156a |
| children | 692abbec9eec |
| files | c_calls.xml |
| diffstat | 1 files changed, 0 insertions(+), 48 deletions(-) [+] |
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--- a/c_calls.xml Mon Feb 20 06:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="conifer_call" name="CoNIFER CNVs caller" version="1.0"> - <description></description> - <command interpreter="python"> - conifer.py call - --input $input - --output temporary - --threshold $threshold - 2>&1 - && awk '{print \$2,\$3,\$4,\$5,\$1}' OFS="\t" temporary > $outputFile - </command> - <inputs> - <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (HDF5)" /> - <param name="threshold" type="float" value="1.5" label="Threshold" /> - </inputs> - <outputs> - <data format="bed" name="outputFile" label="${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>