Mercurial > repos > ppericard > viscorvar
view computeMatSimilarity_wrapper.R @ 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author | ppericard |
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date | Tue, 23 Jun 2020 19:57:35 -0400 |
parents | |
children | e93350dc99f1 |
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#!/usr/bin/env Rscript # Setup R error handling to go to stderr options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) # we need that to not crash galaxy with an UTF8 error on German LC settings. loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") ## Get parameters ## suppressPackageStartupMessages(require(argparse)) parser <- ArgumentParser(description='Run the computeMatSimilarity function') parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") args <- parser$parse_args() ## Print parameters print("Input RData:") print(args$input_rdata) print("Output RData:") print(args$output_rdata) ## Loading libraries # suppressPackageStartupMessages(require(mixOmics)) # R script call source_local <- function(fname) { argv <- commandArgs(trailingOnly = FALSE) base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) source(paste(base_dir, fname, sep="/")) } ## Loading local functions # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) suppressPackageStartupMessages(require(visCorVar)) print("visCorVar has been loaded") # Loading input Rdata file # loads res_matCorAddVar object load(args$input_rdata) # Run main function res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar) liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar save(res_compute_mat_similarity, file = args$output_rdata)