diff xcms_plot_chromatogram.r @ 17:9fff8c8ab4a3 draft

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

--- a/xcms_plot_chromatogram.r	Wed Apr 07 10:31:10 2021 +0000
+++ b/xcms_plot_chromatogram.r	Mon Jul 15 15:54:03 2024 +0000
@@ -6,19 +6,21 @@
 
 #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")
 
@@ -52,10 +54,12 @@
 
 register(SerialParam())
 if (!exists("chromTIC") || is.null(chromTIC)) {
-  cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum")
+  cat("\t\t\tCompute TIC\n")
+  chromTIC <- chromatogram(xdata, aggregationFun = "sum")
 }
 if (!exists("chromBPI") || is.null(chromBPI)) {
-  cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max")
+  cat("\t\t\tCompute BPI\n")
+  chromBPI <- chromatogram(xdata, aggregationFun = "max")
 }
 
 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted