diff TableMerge/tablemerge_wrap.R @ 0:902ab790fb7b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TableMerge/tablemerge_wrap.R	Thu Feb 23 04:37:49 2017 -0500
@@ -0,0 +1,38 @@
+#!/usr/bin/Rscript --vanilla --slave --no-site-file
+
+################################################################################################
+# WRAPPER FOR tablemerge_script.R (TABLE MERGE)                                                #
+#                                                                                              #
+# Author: Melanie PETERA                                                                       #
+# User: Galaxy                                                                                 #
+# Original data: used with tablemerge_script.R                                                 #
+# Starting date: 11-05-2015                                                                    #
+# V-1: Firt version of wrapper                                                                 #
+#                                                                                              #
+#                                                                                              #
+# Input files: dataMatrix ; Metadata file                                                      #
+# Output files: dataMatrix ; Metadata 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("tablemerge_script.R","RcheckLibrary.R","miniTools.R")
+
+
+if(length(args) < 4){ stop("NOT enough argument !!!") }
+
+
+tab.merge(args$dataMatrix_in, args$Metadata_in, args$metatype, args$combined_out)
+
+
+#delete the parameters to avoid the passage to the next tool in .RData image
+rm(args)