--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/networkVar_wrapper.R	Fri Oct 25 07:10:59 2019 -0400
@@ -0,0 +1,79 @@
+#!/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 networkVar function')
+
+parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file")
+parser$add_argument('--block_splsda_rdata', dest='block_splsda_rdata', required=TRUE, help="block.splsda RData file")
+parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file")
+parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file")
+parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
+parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml")
+
+args <- parser$parse_args()
+
+## Print parameters
+print("matSimilarity RData file:")
+print(args$mat_similarity_rdata)
+print("block.splsda RData file:")
+print(args$block_splsda_rdata)
+print("Variables list file:")
+print(args$var_list_file)
+print("Variables of interest:")
+print(args$interest_var_file)
+print("Response variables:")
+print(args$responses_var)
+print("Output graphml:")
+print(args$output_graph)
+
+## Loading libraries
+suppressPackageStartupMessages(require(mixOmics))
+suppressPackageStartupMessages(require(igraph))
+
+# R script call
+source_local <- function(fname)
+{
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+## Loading local functions
+source_local("Integration_block_splsda_fonc.R")
+
+load(args$mat_similarity_rdata)
+load(args$block_splsda_rdata)
+
+variables_vector = as.character(read.table(args$var_list_file, header=FALSE)[[1]])
+interest_var_vec = NULL
+
+if (args$interest_var_file != 'None') {
+    interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
+}
+
+response_variables = strsplit(args$responses_var, ",")[[1]]
+
+print("Variables vector:")
+print(variables_vector)
+print("interest_var_vec:")
+print(interest_var_vec)
+print("response_variables:")
+print(response_variables)
+
+network = networkVar(liste_matSimilarity_group = liste_matSimilarity_group,
+                     comp = comp,
+                     res_block_splsda = mixomics_result,
+                     cutoff_comp = 0.8,
+                     vec_varBlock = variables_vector,
+                     vec_varRep = response_variables,
+                     vec_varBlockInteret = interest_var_vec,
+                     cutoff = 0)
+
+write.graph(network$gR, file = args$output_graph, format = "graphml")