--- a/xcms_export_samplemetadata.r	Wed Apr 07 09:53:54 2021 +0000
+++ b/xcms_export_samplemetadata.r	Mon Sep 11 09:14:35 2023 +0000
@@ -2,26 +2,28 @@
 
 #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("xcms", "batch")
 loadAndDisplayPackages(pkgs)
-cat("\n\n");
+cat("\n\n")
 
 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
 
 
 sampleMetadata <- NULL
 for (image in args$images) {
-    load(image)
-    if (exists("raw_data")) xdata <- raw_data
-    if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
-    if (is.null(sampleMetadata))
-        sampleMetadata <- xdata@phenoData@data
-    else
-        sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data)
+  load(image)
+  if (exists("raw_data")) xdata <- raw_data
+  if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+  if (is.null(sampleMetadata))
+    sampleMetadata <- xdata@phenoData@data
+  else
+    sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data)
 }
 colnames(sampleMetadata) <- c("sample_name", "class")
 sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name)