--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viscorvar_computematsimilarity.R	Fri Oct 23 10:15:56 2020 +0000
@@ -0,0 +1,50 @@
+#!/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$output_rdata)
+
+## Loading libraries
+# suppressPackageStartupMessages(require(mixOmics))
+
+# R script call
+source_local <- function(fname)
+{
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+
+## Loading local functions
+suppressPackageStartupMessages(require(visCorVar))
+
+# Loading input Rdata file
+# loads res_matCorAddVar object
+load(args$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)
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