Mercurial > repos > ppericard > viscorvar
comparison viscorvar_computematsimilarity.R @ 2:c8533e9298e5 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
| author | ppericard |
|---|---|
| date | Fri, 23 Oct 2020 10:15:56 +0000 |
| parents | |
| children |
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| 1:e93350dc99f1 | 2:c8533e9298e5 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 # Setup R error handling to go to stderr | |
| 4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 5 | |
| 6 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
| 7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 8 | |
| 9 ## Get parameters ## | |
| 10 suppressPackageStartupMessages(require(argparse)) | |
| 11 | |
| 12 parser <- ArgumentParser(description='Run the computeMatSimilarity function') | |
| 13 | |
| 14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") | |
| 15 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") | |
| 16 | |
| 17 args <- parser$parse_args() | |
| 18 | |
| 19 ## Print parameters | |
| 20 print("Input RData:") | |
| 21 print(args$input_rdata) | |
| 22 print("Output RData:") | |
| 23 print(args$output_rdata) | |
| 24 | |
| 25 ## Loading libraries | |
| 26 # suppressPackageStartupMessages(require(mixOmics)) | |
| 27 | |
| 28 # R script call | |
| 29 source_local <- function(fname) | |
| 30 { | |
| 31 argv <- commandArgs(trailingOnly = FALSE) | |
| 32 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 33 source(paste(base_dir, fname, sep="/")) | |
| 34 } | |
| 35 | |
| 36 ## Loading local functions | |
| 37 suppressPackageStartupMessages(require(visCorVar)) | |
| 38 | |
| 39 # Loading input Rdata file | |
| 40 # loads res_matCorAddVar object | |
| 41 load(args$input_rdata) | |
| 42 | |
| 43 # Run main function | |
| 44 res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar) | |
| 45 | |
| 46 liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group | |
| 47 res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar | |
| 48 | |
| 49 save(res_compute_mat_similarity, | |
| 50 file = args$output_rdata) |