diff xcms_plot_chromatogram.r @ 18:4631c19a75ff draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163

--- a/xcms_plot_chromatogram.r	Mon Jul 15 15:54:03 2024 +0000
+++ b/xcms_plot_chromatogram.r	Mon Feb 03 14:40:09 2025 +0000
@@ -4,11 +4,11 @@
 # ----- PACKAGE -----
 cat("\tSESSION INFO\n")
 
-#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")
 
@@ -19,7 +19,7 @@
 
 # ----- ARGUMENTS -----
 cat("\tARGUMENTS INFO\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
 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
 
 cat("\n\n")
@@ -54,12 +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