diff xcms_retcor.r @ 50:0bc08f128b42 draft default tip

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

--- a/xcms_retcor.r	Mon Jul 15 15:55:13 2024 +0000
+++ b/xcms_retcor.r	Mon Feb 03 14:41:19 2025 +0000
@@ -9,11 +9,11 @@
 # ----- 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")
 
@@ -24,7 +24,7 @@
 
 # ----- 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")
@@ -32,7 +32,7 @@
 # ----- PROCESSING INFILE -----
 cat("\tARGUMENTS PROCESSING INFO\n")
 
-#saving the specific parameters
+# saving the specific parameters
 method <- args$method
 
 cat("\n\n")
@@ -41,7 +41,7 @@
 # ----- ARGUMENTS PROCESSING -----
 cat("\tINFILE PROCESSING INFO\n")
 
-#image is an .RData file necessary to use xset variable given by previous tools
+# image is an .RData file necessary to use xset variable given by previous tools
 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.*")
@@ -70,9 +70,9 @@
 print(adjustRtimeParam)
 
 if (hasAdjustedRtime(xdata)) {
-  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
-  cat("Replace raw retention times with adjusted retention times.\n")
-  xdata <- applyAdjustedRtime(xdata)
+    cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+    cat("Replace raw retention times with adjusted retention times.\n")
+    xdata <- applyAdjustedRtime(xdata)
 }
 xdata <- adjustRtime(xdata, param = adjustRtimeParam)
 
@@ -97,7 +97,7 @@
 print(xset)
 cat("\n\n")
 
-#saving R data in .Rdata file to save the variables used in the present tool
+# saving R data in .Rdata file to save the variables used in the present tool
 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")