Mercurial > repos > bzonnedda > conifer2
changeset 7:5dcedbe7edff draft
Uploaded
author | bzonnedda |
---|---|
date | Mon, 20 Feb 2017 06:32:30 -0500 |
parents | 063348f7c3e4 |
children | 4e5df703320f |
files | c_calls.xml |
diffstat | 1 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/c_calls.xml Mon Feb 20 06:32:30 2017 -0500 @@ -0,0 +1,48 @@ +<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>