--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA_combinexsAnnos.r	Fri Jul 26 16:49:18 2019 -0400
@@ -0,0 +1,72 @@
+#!/usr/bin/env Rscript
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+#Import the different functions
+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+source_local("lib.r")
+
+pkgs=c("CAMERA","multtest","batch")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
+
+cat("\n\n");
+
+
+# ----- PROCESSING INFILE -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image_pos)
+xaP=xa
+
+diffrepP=NULL
+if (exists("diffrep")) diffrepP=diffrep
+
+load(args$image_neg)
+xaN=xa
+
+diffrepN=NULL
+if (exists("diffrep")) diffrepN=diffrep
+
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+# Save arguments to generate a report
+if (!exists("listOFargs")) listOFargs=list()
+listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args
+
+cat("\n\n")
+
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+cAnnot=combinexsAnnos_function(
+    xaP=xaP,xaN=xaN,
+    diffrepP=diffrepP, diffrepN=diffrepN,
+    pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta,
+    convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT,
+    variableMetadataOutput="variableMetadata.tsv"
+)
+
+# ----- EXPORT -----
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
+save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData")
+
+cat("\n\n")
+
+cat("\tDONE\n")