Mercurial > repos > bzonnedda > conifer2
view c_rpkm.xml @ 22:15d60c7c9a19 draft
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author | bzonnedda |
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date | Wed, 05 Jul 2017 13:02:55 -0400 |
parents | 7f685fe845e1 |
children | 02091c92f4f1 |
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<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0"> <description></description> <command> mkdir rpkm_dir; #for $input_bam in $inputs: #if str($input_bam.label.value) != "": ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam; ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai; python '$__tool_directory__/conifer.py' rpkm --probes $probesFile --input ${$input_bam.label.value}.bam --output rpkm_dir/${$input_bam.label.value}.txt; #else ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam; ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai; python '$__tool_directory__/conifer.py' rpkm --probes $probesFile --input ${input_bam.inputFile.dataset.name}.bam --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt; #end if #end for python '$__tool_directory__/conifer.py' analyze --probes $probesFile --rpkm_dir rpkm_dir --output $outputFile --svd $svd 2>&1; </command> <inputs> <param format="bed" name="probesFile" type="data" label="Target regions (BED)" /> <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below."> <param format="bam" name="inputFile" type="data" label="BAM file" /> <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead"> <validator type="regex" message="Spaces are not allowed">^\S*$</validator> </param> </repeat> <param name="svd" type="integer" value="2" label="SVD" /> </inputs> <outputs> <data format="hdf5" name="outputFile" label="${tool.name} on ${on_string}: hdf5" /> </outputs> <help> .. class:: warningmark **Warning about SVD** The SVD value must be less than the number of samples. E.g.: if the number of samples is 3, the value of SVD must be 2 or less. **What it does** This tool calculates RPKM for each BAM file and analyzes them, afterward it creates a unique HDF5 file containing all SVD-ZRPKM values, probes and samples for downstream analysis with 'CoNIFER CNV caller' and 'CoNIFER plot'. **License and citation** This Galaxy tool is Copyright © 2015 `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>