--- a/xcms_refine.r	Mon Jul 15 16:00:52 2024 +0000
+++ b/xcms_refine.r	Mon Feb 03 14:46:55 2025 +0000
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 # ----- LOG FILE -----
-log_file <- file("log.txt", open  =  "wt")
+log_file <- file("log.txt", open = "wt")
 sink(log_file)
 sink(log_file, type = "output")
 
@@ -9,11 +9,11 @@
 # ----- PACKAGE -----
 cat("\tSESSION INFO\n")
 
-#Import the different functions
+# 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 = "/"))
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
 }
 source_local("lib.r")
 
@@ -32,23 +32,23 @@
 # ----- PROCESSING INFILE -----
 cat("\tARGUMENTS PROCESSING INFO\n")
 
-#saving the specific parameters
-args_method  <- args$method
-args_image   <- args$image
+# saving the specific parameters
+args_method <- args$method
+args_image <- args$image
 args_msLevel <- args$msLevel
 param_args <- list()
 
 if (args_method == "CleanPeaks") {
-  param_args$maxPeakwidth <- args$maxPeakwidth
+    param_args$maxPeakwidth <- args$maxPeakwidth
 } else if (args_method == "FilterIntensity") {
-  param_args$threshold <- args$threshold
-  param_args$value <- args$value
-  param_args$nValues <- args$nValues
+    param_args$threshold <- args$threshold
+    param_args$value <- args$value
+    param_args$nValues <- args$nValues
 } else if (args_method == "MergeNeighboringPeaks") {
-  param_args$expandRt <- args$expandRt
-  param_args$expandMz <- args$expandMz
-  param_args$ppm      <- args$ppm
-  param_args$minProp  <- args$minProp
+    param_args$expandRt <- args$expandRt
+    param_args$expandMz <- args$expandMz
+    param_args$ppm <- args$ppm
+    param_args$minProp <- args$minProp
 }
 
 cat("\n\n")
@@ -57,7 +57,7 @@
 # ----- ARGUMENTS PROCESSING -----
 cat("\tINFILE PROCESSING INFO\n")
 
-#image is an .RData file necessary to use xset variable given by previous tools
+# image is an .RData file necessary to use xset variable given by previous tools
 load(args_image)
 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
 
@@ -78,20 +78,20 @@
 cat("\t\tPREPARE PARAMETERS\n\n")
 
 if (args_method == "CleanPeaks") {
-  refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
+    refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
 } else if (args_method == "FilterIntensity") {
-  refineChromPeaksParam <- FilterIntensityParam(
-    threshold = param_args$threshold,
-    nValues = param_args$nValues,
-    value = param_args$value
-  )
+    refineChromPeaksParam <- FilterIntensityParam(
+        threshold = param_args$threshold,
+        nValues = param_args$nValues,
+        value = param_args$value
+    )
 } else if (args_method == "MergeNeighboringPeaks") {
-  refineChromPeaksParam <- MergeNeighboringPeaksParam(
-    expandRt = param_args$expandRt,
-    expandMz = param_args$expandMz,
-    ppm = param_args$ppm,
-    minProp = param_args$minProp
-  )
+    refineChromPeaksParam <- MergeNeighboringPeaksParam(
+        expandRt = param_args$expandRt,
+        expandMz = param_args$expandMz,
+        ppm = param_args$ppm,
+        minProp = param_args$minProp
+    )
 }
 
 cat(str(refineChromPeaksParam))
@@ -116,7 +116,7 @@
 print(xset)
 cat("\n\n")
 
-#saving R data in .Rdata file to save the variables used in the present tool
+# saving R data in .Rdata file to save the variables used in the present tool
 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")