diff xcms_fillpeaks.r @ 25:26d77e9ceb49 draft

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

--- a/xcms_fillpeaks.r	Wed Feb 12 08:28:33 2020 -0500
+++ b/xcms_fillpeaks.r	Wed Apr 07 10:34:07 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")
+pkgs <- c("xcms", "batch")
 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")
 
@@ -53,7 +55,7 @@
 # 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
 
@@ -68,15 +70,15 @@
 
 cat("\t\t\tFilling missing peaks using default settings\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()))]
 
-fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
+fillChromPeaksParam <- do.call(paste0(method, "Param"), args)
 print(fillChromPeaksParam)
 
 # back compatibility between xcms-3.0.0 and xcms-3.5.2
 xdata <- updateObject(xdata)
 register(SerialParam())
-xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
+xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam)
 
 if (exists("intval")) {
     getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
@@ -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="fillpeaks.RData")
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
+save(list = objects2save[objects2save %in% ls()], file = "fillpeaks.RData")
 
 cat("\n\n")