diff ipo4retgroup.r @ 10:57f180a8eaae draft default tip

planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11

--- a/ipo4retgroup.r	Mon Dec 16 10:26:13 2019 +0000
+++ b/ipo4retgroup.r	Mon Sep 11 22:36:51 2023 +0000
@@ -1,47 +1,49 @@
 #!/usr/bin/env Rscript
-#Authors Gildas Le Corguille and Yann Guitton
+# Authors Gildas Le Corguille and Yann Guitton
 
 
 # ----- PACKAGE -----
 cat("\tSESSION INFO\n")
 
-#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="/")) }
+# 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 = "/"))
+}
 source_local("lib.r")
 
-pkgs <- c("IPO","batch")
+pkgs <- c("IPO", "batch")
 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')
+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");
-
-
+cat("\n\n")
 # ----- PROCESSING INFILE -----
 cat("\tARGUMENTS PROCESSING INFO\n")
 
-samplebyclass = 2
-if (!is.null(args$samplebyclass)){
-  samplebyclass = args$samplebyclass; args$samplebyclass=NULL
+samplebyclass <- 2
+if (!is.null(args$samplebyclass)) {
+  samplebyclass <- args$samplebyclass
+  args$samplebyclass <- NULL
 }
 
 cat("\n\n")
 
 # ----- INFILE PROCESSING -----
 cat("\tINFILE PROCESSING INFO\n")
-options(bitmapType='cairo')
+options(bitmapType = "cairo")
 
-#image is an .RData file necessary to use xset variable given by previous tools
-load(args$image); args$image=NULL
+# image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+args$image <- NULL
 
 # Because so far CAMERA isn't compatible with the new XCMSnExp object
-if (exists("xdata")){
-    xset <- getxcmsSetObject(xdata)
+if (exists("xdata")) {
+  xset <- getxcmsSetObject(xdata)
 }
 
 if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData")
@@ -52,7 +54,7 @@
 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
 singlefile <- rawFilePath$singlefile
 print(singlefile)
-directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)
+directory <- retrieveRawfileInWD(singlefile, NULL)
 
 
 cat("\n\n")