--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GalFilter/filter_wrap.R	Thu Feb 23 04:39:36 2017 -0500
@@ -0,0 +1,63 @@
+#!/usr/bin/Rscript --vanilla --slave --no-site-file
+
+################################################################################################
+# WRAPPER FOR filter_script.R (GENERIC FILTERS)                                                #
+#                                                                                              #
+# Author: Melanie PETERA based on Marion LANDI's filters' wrapper                              #
+# User: Galaxy                                                                                 #
+# Original data: used with filter_script.R                                                     #
+# Starting date: 04-09-2014                                                                    #
+# V-1: Restriction of old filter wrapper to Filter according to factors                        #
+# V-1.1: Modification to allow the choice of meta-data table for filtering                     #
+# V-2: Addition of numerical filter                                                            #
+#                                                                                              #
+#                                                                                              #
+# Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                      #
+# Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                     #
+#                                                                                              #
+################################################################################################
+
+
+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("filter_script.R","RcheckLibrary.R","miniTools.R")
+
+
+if(length(args) < 8){ stop("NOT enough argument !!!") }
+
+list_num <- NULL
+if(!is.null(args$parm_col)){
+	for( i in which(names(args)=="num_file") ){
+		if(args[[i+2]] %in% c("lower","upper")){
+		  list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]])))
+		}
+		if(args[[i+2]] %in% c("between","extremity")){
+		  list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]],args[[i+4]])))
+		}
+	}
+}	
+
+list_fact <- NULL
+if(!is.null(args$factor_col)){
+	for( i in which(names(args)=="qual_file") ){
+		list_fact <- c(list_fact, list(c(args[[i+1]], args[[i+2]], args[[i]])))
+	}
+}	
+
+filters(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in,
+        args$Numeric, list_num, args$Factors, list_fact,
+        args$dataMatrix_out, args$sampleMetadata_out, args$variableMetadata_out)
+
+#filters(ion.file.in, meta.samp.file.in, meta.ion.file.in,
+#        NUM, ls.num, FACT, ls.fact,
+#        ion.file.out, meta.samp.file.out, meta.ion.file.out)
+
+#delete the parameters to avoid the passage to the next tool in .RData image
+rm(args)