--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA_groupFWHM.R	Sun Nov 24 21:28:57 2024 +0000
@@ -0,0 +1,142 @@
+#!/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", "xcms", "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 = FALSE, quote = FALSE, sep = "\t")
+
+cat("\n\n")
+
+print("Arguments retrieved from the command line:")
+print(args)
+
+# Function to convert "NA" strings to actual NA values and string lists to numeric lists
+convertStringToNumeric <- function(x) {
+  # Force conversion to character
+  x <- as.character(x)
+
+  if (x == "NA") {
+    return(NA)
+  } else if (grepl("^[0-9]+$", x)) {
+    # If the string represents a single numeric value
+    return(as.numeric(x))
+  } else {
+    # Convert string representation of a list to a numeric vector
+    # Use a regular expression to split by common separators
+    return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
+  }
+}
+
+# Convert only the 'sample' element in args
+args$sample <- convertStringToNumeric(args$sample)
+
+print("Argument types:")
+print(sapply(args, class))
+
+# Check if the image file exists
+if (!file.exists(args$image)) {
+  stop("The RData file does not exist: ", args$image)
+}
+
+# ----- PROCESSING INFILE -----
+
+# Load the RData file (it should contain the xset object, typically an xcmsSet or XCMSnExp)
+load(args$image)
+args$image <- NULL
+
+# Save arguments to generate a report
+if (!exists("listOFlistArguments")) listOFlistArguments <- list()
+listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_groupFWHM")]] <- args
+
+# We unzip automatically the chromatograms from the zip files.
+if (!exists("zipfile")) zipfile <- NULL
+if (!exists("singlefile")) singlefile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+args <- rawFilePath$args
+
+print(paste("singlefile :", singlefile))
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
+
+# If the xdata object exists, convert it to xcmsSet
+if (exists("xdata")) {
+  phenoData <- xdata@phenoData
+  xset <- getxcmsSetObject(xdata)
+}
+
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+# Verification of a group step before doing the fillpeaks job.
+if (dim(xdata@phenoData@data)[1] > 1) {
+  if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the groupFWHM step")
+} else {
+  print("Only one file in the phenoData keep xset as is")
+}
+
+# Convert the xset object to xsAnnotate using CAMERA
+cat("Converting xset object to xsAnnotate...\n")
+xsa <- xsAnnotate(xset, sample = args$sample, nSlaves = as.numeric(args$nSlaves), polarity = args$polarity)
+
+print(paste0("All samples in xset object: ", paste(seq_along(xset@filepaths), collapse = ", ")))
+print(paste0("Selected samples: ", paste(xsa@sample, collapse = ", ")))
+print(paste0("Run in parallel mode (0 = disabled): ", paste(xsa@runParallel)))
+print(paste0("Polarity: ", xsa@polarity))
+
+# Apply the groupFWHM function with the parameters
+cat("Applying groupFWHM...\n")
+xa <- groupFWHM(xsa, sigma = as.numeric(args$sigma), perfwhm = as.numeric(args$perfwhm), intval = args$intval)
+
+# Extract the list of annotated peaks
+peakList <- getPeaklist(xa, intval = args$intval)
+
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
+  names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
+
+if (!exists("RTinMinute")) RTinMinute <- FALSE
+
+if (args$convertRTMinute && RTinMinute == FALSE) {
+  RTinMinute <- TRUE
+  variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
+}
+
+# Save the peak list to a TSV file
+output_file_tsv <- "variableMetadata.tsv"
+write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE)
+
+# Save the xsAnnotate object
+output_file_RData <- "camera_fwhm.RData"
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
+save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
+
+cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")