diff xcms_group.r @ 27:d45a786cbc40 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

--- a/xcms_group.r	Tue Jul 21 09:17:27 2020 -0400
+++ b/xcms_group.r	Wed Apr 07 12:06:33 2021 +0000
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 # ----- LOG FILE -----
-log_file=file("log.txt", open = "wt")
+log_file <- file("log.txt", open = "wt")
 sink(log_file)
 sink(log_file, type = "output")
 
@@ -10,18 +10,20 @@
 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="/")) }
+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("xcms","batch","RColorBrewer")
+pkgs <- c("xcms", "batch", "RColorBrewer")
 loadAndDisplayPackages(pkgs)
 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 = F, quote = F, sep = "\t")
 
 cat("\n\n")
 
@@ -50,7 +52,7 @@
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 
@@ -65,12 +67,12 @@
 
 
 cat("\t\t\tPerform the correspondence\n")
-args$sampleGroups = xdata$sample_group
+args$sampleGroups <- xdata$sample_group
 
 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
-args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list(sampleGroups=c(1,2))))]
+args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list(sampleGroups = c(1, 2))))]
 
-groupChromPeaksParam <- do.call(paste0(method,"Param"), args)
+groupChromPeaksParam <- do.call(paste0(method, "Param"), args)
 print(groupChromPeaksParam)
 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
 
@@ -97,8 +99,8 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
-save(list=objects2save[objects2save %in% ls()], file="group.RData")
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
+save(list = objects2save[objects2save %in% ls()], file = "group.RData")
 
 cat("\n\n")