diff xcms_retcor.r @ 49:177b5847a211 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253

--- a/xcms_retcor.r	Wed Apr 07 10:31:56 2021 +0000
+++ b/xcms_retcor.r	Mon Jul 15 15:55:13 2024 +0000
@@ -11,19 +11,21 @@
 
 #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", "RColorBrewer")
 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")
 
@@ -40,7 +42,8 @@
 cat("\tINFILE PROCESSING INFO\n")
 
 #image is an .RData file necessary to use xset variable given by previous tools
-load(args$image); args$image <- NULL
+load(args$image)
+args$image <- NULL
 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.*")
 
 # Handle infiles