--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA_annotateDiffreport.r	Thu Aug 29 11:38:21 2019 -0400
@@ -0,0 +1,78 @@
+#!/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$image); args$image=NULL
+
+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_annotatediff")]] = args
+
+# We unzip automatically the chromatograms from the zip files.
+if (!exists("zipfile")) zipfile=NULL
+if (!exists("singlefile")) singlefile=NULL
+rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile = rawFilePath$zipfile
+singlefile = rawFilePath$singlefile
+args = rawFilePath$args
+directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+# Because so far CAMERA isn't compatible with the new XCMSnExp object
+if (exists("xdata")){
+    xset <- getxcmsSetObject(xdata)
+}
+
+cat("\n\n")
+
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
+xa=results_list$xa
+diffrep=results_list$diffrep
+variableMetadata=results_list$variableMetadata
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXSET OBJECT INFO\n")
+print(xa)
+cat("\n\n")
+
+#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="annotatediff.RData")
+
+cat("\n\n")
+
+cat("\tDONE\n")