Mercurial > repos > bzonnedda > conifer2
changeset 0:9e24f334dc80 draft
Uploaded
author | bzonnedda |
---|---|
date | Mon, 06 Feb 2017 10:55:13 -0500 |
parents | |
children | 54973c4a1125 |
files | c_rpkm.xml |
diffstat | 1 files changed, 82 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/c_rpkm.xml Mon Feb 06 10:55:13 2017 -0500 @@ -0,0 +1,82 @@ +<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 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 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 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>