diff xcms_retcor.r @ 25:aa252eec9229 draft

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

--- a/xcms_retcor.r	Wed Jul 29 05:10:58 2020 -0400
+++ b/xcms_retcor.r	Wed Apr 07 12:08:25 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")
 
@@ -38,13 +40,13 @@
 cat("\tINFILE PROCESSING INFO\n")
 
 #image is an .RData file necessary to use xset variable given by previous tools
-load(args$image); args$image=NULL
+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.*")
 
 # 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
 
@@ -59,9 +61,9 @@
 
 cat("\t\t\tAlignment/Retention Time correction\n")
 # 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()))]
+args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
 
-adjustRtimeParam <- do.call(paste0(method,"Param"), args)
+adjustRtimeParam <- do.call(paste0(method, "Param"), args)
 print(adjustRtimeParam)
 
 if (hasAdjustedRtime(xdata)) {
@@ -69,11 +71,7 @@
   cat("Replace raw retention times with adjusted retention times.\n")
   xdata <- applyAdjustedRtime(xdata)
 }
-xdata <- adjustRtime(xdata, param=adjustRtimeParam)
-
-#cat("\t\t\tCompute and Store TIC and BPI\n")
-#chromTIC_adjusted = chromatogram(xdata, aggregationFun = "sum")
-#chromBPI_adjusted = chromatogram(xdata, aggregationFun = "max")
+xdata <- adjustRtime(xdata, param = adjustRtimeParam)
 
 cat("\n\n")
 
@@ -97,8 +95,8 @@
 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="retcor.RData")
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")
 
 cat("\n\n")