--- a/xcms_export_samplemetadata.r	Mon Jul 15 15:57:52 2024 +0000
+++ b/xcms_export_samplemetadata.r	Mon Feb 03 14:43:55 2025 +0000
@@ -1,10 +1,10 @@
 #!/usr/bin/env Rscript
 
-#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")
 
@@ -12,18 +12,19 @@
 loadAndDisplayPackages(pkgs)
 cat("\n\n")
 
-args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
+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)