Mercurial > repos > iuc > scater_create_qcmetric_ready_sce
comparison scater-normalize.R @ 0:2d455a7e8a3d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
| author | iuc |
|---|---|
| date | Thu, 18 Jul 2019 11:14:06 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:2d455a7e8a3d |
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| 1 #!/usr/bin/env Rscript | |
| 2 #Normalises a SingleCellExperiment object | |
| 3 | |
| 4 # Load optparse we need to check inputs | |
| 5 library(optparse) | |
| 6 library(workflowscriptscommon) | |
| 7 library(LoomExperiment) | |
| 8 library(scater) | |
| 9 | |
| 10 # parse options | |
| 11 option_list = list( | |
| 12 make_option( | |
| 13 c("-i", "--input-loom"), | |
| 14 action = "store", | |
| 15 default = NA, | |
| 16 type = 'character', | |
| 17 help = "A SingleCellExperiment object file in Loom format." | |
| 18 ), | |
| 19 make_option( | |
| 20 c("-o", "--output-loom"), | |
| 21 action = "store", | |
| 22 default = NA, | |
| 23 type = 'character', | |
| 24 help = "File name in which to store the SingleCellExperiment object in Loom format." | |
| 25 ) | |
| 26 ) | |
| 27 | |
| 28 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom')) | |
| 29 | |
| 30 # Check parameter values | |
| 31 | |
| 32 if ( ! file.exists(opt$input_loom)){ | |
| 33 stop((paste('File', opt$input_loom, 'does not exist'))) | |
| 34 } | |
| 35 | |
| 36 # Input from Loom format | |
| 37 | |
| 38 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') | |
| 39 print(paste("Normalising....")) | |
| 40 | |
| 41 #Normalise | |
| 42 scle <- normalize(scle, exprs_values = 1) | |
| 43 | |
| 44 print(paste("Finished normalising")) | |
| 45 | |
| 46 # Output to a Loom file | |
| 47 if (file.exists(opt$output_loom)) { | |
| 48 file.remove(opt$output_loom) | |
| 49 } | |
| 50 export(scle, opt$output_loom, format='loom') |