--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CorrTable/Corr_wrap.r	Thu Oct 11 05:35:55 2018 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/Rscript --vanilla --slave --no-site-file
+
+################################################################################################
+# WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE)                                    #
+#                                                                                              #
+# Author: Ophelie BARBET                                                                       #
+# User: Galaxy                                                                                 #
+# Original data: used with Corr_Script_samples_row.R                                           #
+# Starting date:                                                                               #
+# V-1: First version of wrapper                                                                #
+#                                                                                              #
+#                                                                                              #
+# Input files: 2 tables with common samples file                                               #
+# Output files: Correlation table ; Heatmap file                                               #
+#                                                                                              #
+################################################################################################
+
+
+library(batch) #necessary for parseCommandArgs function
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+
+source_local <- function(...){
+	argv <- commandArgs(trailingOnly = FALSE)
+	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+	for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
+}
+#Import the different functions
+source_local("Corr_Script_samples_row.R")
+
+
+if(length(args) < 10){ stop("NOT enough argument !!!") }
+
+
+cat('\n--------------------------------------------------------------------', 
+'\nParameters used in "Between-table Correlation":\n\n')
+print(args)
+cat('--------------------------------------------------------------------\n\n')
+
+
+risk_alpha <- NULL
+correct_multi <- NULL
+if(args$test_corr == "yes"){
+	risk_alpha <- args$risk_alpha
+	correct_multi <- args$correct_multi
+}
+
+filters_choice <- NULL
+threshold <- NULL
+if(args$filter == "yes"){
+	filters_choice <- args$filters_choice
+	if(filters_choice == "filters_0_thr"){
+		threshold <- args$threshold
+	}	
+}
+
+type_classes <- NULL
+reg_class_value <- NULL
+irreg_class_vect <- NULL
+if(args$color_heatmap == "yes"){
+	type_classes <- args$type_classes
+	if(type_classes == "regular"){
+		reg_class_value <- args$reg_class_value
+	} else if(type_classes == "irregular"){
+		irreg_class_vect <- eval(parse(text=paste0("c",args$irreg_class_vect)))		
+	}
+}	
+
+
+correlation.tab(args$tab1_in, args$tab2_in, args$tab1_samples, args$tab2_samples, args$corr_method, args$test_corr, risk_alpha, correct_multi, args$filter, filters_choice, threshold,
+args$reorder_var, args$color_heatmap, type_classes, reg_class_value, irreg_class_vect, args$tabcorr_out, args$heatmap_out)
+
+
+cat('\n--------------------------------------------------------------------',
+'\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
+sessionInfo()
+cat('--------------------------------------------------------------------\n\n')
+
+
+#delete the parameters to avoid the passage to the next tool in .RData image
+rm(args)
\ No newline at end of file