--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS_plot.r	Wed Jul 03 05:08:14 2019 -0400
@@ -0,0 +1,152 @@
+#!/usr/bin/env Rscript
+# metaMS_plot.r version="1.0.0"
+#created by Yann GUITTON and updated by Julien SAINT-VANNE
+
+
+# ----- LOG FILE -----
+#log_file <- file("log.txt", open = "wt")
+#sink(log_file)
+#sink(log_file, type = "output")
+
+
+# ----- 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_metams.r")
+
+pkgs <- c("metaMS","batch") #"batch" necessary for parseCommandArgs function
+loadAndDisplayPackages(pkgs)
+
+cat("\n")
+
+modNamC <- "plot_metaMS" ## module name
+
+cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n\n", sep="")
+
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n\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\t')
+print(cbind(value = unlist(args)))
+
+
+# ----- PROCESSING INFILE -----
+cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
+
+# Loading RData file
+load(args$metaMS)
+if (!exists("resGC")) stop("\n\nERROR: The RData doesn't contain any object called 'resGC' which is provided by the tool: new_metaMS.runGC")
+
+if(args$selecteic) {
+    #Unknown EIC parameter
+    if (args$unkn[1] != "NULL") {
+        #When unkn = 0 user want to process all unknowns
+        if(args$unkn[1] == 0) {
+            args$unkn <- c(1:nrow(resGC$PeakTable))
+            print("User want to process on all unknown(s) found in metaMS process")
+        }
+        #TODO find the biggest number of unkn ask by user cause it can write "1,15,9,8" with a max of 11 unkn. With this code it finds the 8 and it will pass
+        #Verify that there is not more user's unkn than metaMS unkn (find in resGC$PeakTable)
+        cat("Number of unknown after metaMS process :",nrow(resGC$PeakTable),"\n")
+        cat("Number of the last unknown ask by user :",args$unkn[length(args$unkn)],"\n")
+        cat("Number of unknown ask by user :",length(args$unkn),"\n")
+        if(args$unkn[length(args$unkn)] <= nrow(resGC$PeakTable)) {
+            unknarg <- args$unkn
+        } else {
+            error_message="Too much unkn compare metaMS results"
+            print(error_message)
+            stop(error_message)
+        }
+    } else {
+        error_message <- "No EIC selected !"
+        print(error_message)
+        stop(error_message)
+    }
+}
+
+cat("\n\n")
+
+
+# ----- INFILE PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n\n")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\n\n\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+#Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata
+
+if(!is.null(singlefile)) {
+    files <- paste("./",names(singlefile),sep="")
+    if(!is.null(files)){
+        if(args$selectbpc){
+            cat("\n\tProcessing BPC(s) from XCMS files...\n")
+            c <- getBPC2s(files = files, xset = xset, rt="raw", pdfname="BPCs_raw.pdf")
+            cat("BPC(s) created...\n")
+        }
+        if(args$selecttic){
+            cat("\n\tProcessing TIC(s) from XCMS files...\n")
+            b <- getTIC2s(files = files, xset = xset, rt="raw", pdfname="TICs_raw.pdf")
+            cat("TIC(s) created...\n")
+        }
+        if(args$selecteic){
+            cat("\n\tProcessing EIC(s) from XCMS files...\n")
+            cat(length(unknarg),"unknown(s) will be process !\n")
+            plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="singlefile")
+            cat("EIC(s) created...\n")
+            #Merge pdf
+            system(paste('gs  -o GCMS_EIC.pdf  -sDEVICE=pdfwrite  -dPDFSETTINGS=/prepress  Unknown_*.pdf'))
+        }
+    } else {
+        error_message <- paste("Can't find",files,"!")
+        print(error_message)
+        stop(error_message)
+    }
+}
+if(!is.null(zipfile)) {
+    files <- getMSFiles(directory)
+    if(!is.null(files)) {
+        if(args$selectbpc) {
+            cat("\n\tProcessing BPC(s) from raw files...\n")
+            c <- getBPC2s(files = files, rt="raw", pdfname="BPCs_raw.pdf")
+            cat("BPC(s) created...\n")
+        }
+        if(args$selecttic) {
+            cat("\n\tProcessing TIC(s) from raw files...\n")
+            b <- getTIC2s(files = files, rt="raw", pdfname="TICs_raw.pdf")  
+            cat("TIC(s) created...\n")
+        }
+        if(args$selecteic) {
+            cat("\n\tProcessing EIC(s) from XCMS files...\n")
+            cat(length(unknarg),"unknown(s) will be process !\n")
+            plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="zipfile")
+            cat("EIC(s) created...\n")
+            #Merge pdf
+            system(paste('gs -sOutputFile=GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf'))
+        }
+    } else {
+        error_message <- paste("Can't find",files,"!")
+        print(error_message)
+        stop(error_message)
+    } 
+}
+
+cat("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "")
\ No newline at end of file