Mercurial > repos > lecorguille > xcms_fillpeaks
diff xcms_fillpeaks.r @ 25:26d77e9ceb49 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
---|---|
date | Wed, 07 Apr 2021 10:34:07 +0000 |
parents | 999f9db0ca2c |
children | bb9ee352fce0 |
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--- 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")