--- a/CAMERA_combinexsAnnos.r	Fri Jul 02 02:52:00 2021 +0000
+++ b/CAMERA_combinexsAnnos.r	Mon Sep 11 22:41:22 2023 +0000
@@ -5,21 +5,23 @@
 
 #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")
 
 pkgs <- c("CAMERA", "multtest", "batch")
 loadAndDisplayPackages(pkgs)
-cat("\n\n");
+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")
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
 
-cat("\n\n");
+cat("\n\n")
 
 
 # ----- PROCESSING INFILE -----
@@ -56,11 +58,11 @@
 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$numDigitsRT,
-    variableMetadataOutput = "variableMetadata.tsv"
+  xaP = xaP, xaN = xaN,
+  diffrepP = diffrepP, diffrepN = diffrepN,
+  pos = args$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 -----