--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matCorAddVar_wrapper.R	Tue Jun 23 19:57:35 2020 -0400
@@ -0,0 +1,115 @@
+#!/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='Compute the matCorEtBlockSelect and addVariablesReponses functions')
+
+parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
+parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="")
+parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file")
+parser$add_argument('--block_Y_file', dest='block_Y_file', required=TRUE, help="Block Y filepath")
+parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
+parser$add_argument('--output_response_var', dest='output_response_var', required=TRUE, help="Output response variables file")
+parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file")
+
+args <- parser$parse_args()
+
+## Print parameters
+print("Input RData:")
+print(args$input_rdata)
+print("Cutoff comp:")
+print(args$cutoff_comp)
+print("Variables of interest:")
+print(args$interest_var_file)
+print("Block Y file:")
+print(args$block_Y_file)
+print("Output RData:")
+print(args$output_rdata)
+print("Output Response variables:")
+print(args$output_response_var)
+print("Output Blocks combinations:")
+print(args$output_blocks_comb)
+
+## Loading libraries
+# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R")
+install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL)
+suppressPackageStartupMessages(require(visCorVar))
+print("visCorVar has been loaded")
+
+# R script call
+source_local <- function(fname)
+{
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+
+# Loading input Rdata file
+load(args$input_rdata)
+
+ncomp = mixomics_result$ncomp
+
+# Reading Block Y matrix
+print("Reading Block Y")
+mat_block_Y = read.table(args$block_Y_file, header=TRUE, row.names=1)
+print(mat_block_Y)
+
+response_var = colnames(mat_block_Y)
+
+print("response_var:")
+print(response_var)
+
+# Write response variables to output file
+invisible(lapply(response_var, write, file=args$output_response_var, append=TRUE, ncolumns=1))
+
+# Reading var of intereset file
+interest_var_vec = NULL
+if (args$interest_var_file != 'None') {
+    interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
+}
+
+#
+comp = 1:2
+
+# Running main function
+res_matCorAddVar = matCorAddVar(res_block_splsda = mixomics_result,
+                                block_Y = mat_block_Y,
+                                cutoff_comp = args$cutoff_comp,
+                                var_interest = interest_var_vec,
+                                comp = comp)
+
+#
+mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1
+mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2
+list_vec_index_block_select  = res_matCorAddVar$list_vec_index_block_select
+list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks
+list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var
+res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest
+
+#
+print("mat_cor_comp1:")
+print(mat_cor_comp1)
+print("mat_cor_comp2:")
+print(mat_cor_comp2)
+print("list_vec_index_block_select:")
+print(list_vec_index_block_select)
+print("list_vec_names_blocks:")
+print(list_vec_names_blocks)
+print("list_cor_comp_selected_var_resp_var:")
+print(list_cor_comp_selected_var_resp_var)
+print("res_compute_cor_var_interest:")
+print(res_compute_cor_var_interest)
+
+# Write all possible blocks combinations to output file
+invisible(lapply(list_vec_names_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=","))
+
+# Save all objects in Rdata output file
+save(res_matCorAddVar,
+     file = args$output_rdata)