Mercurial > repos > lecorguille > xcms_group
diff xcms_group.r @ 30:3820e3f3b1cb draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author | workflow4metabolomics |
---|---|
date | Mon, 03 Feb 2025 14:45:05 +0000 |
parents | 2b676d5eb848 |
children |
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--- a/xcms_group.r Mon Jul 15 15:59:02 2024 +0000 +++ b/xcms_group.r Mon Feb 03 14:45:05 2025 +0000 @@ -9,11 +9,11 @@ # ----- PACKAGE ----- cat("\tSESSION INFO\n") -#Import the different functions +# 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 = "/")) + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep = "/")) } source_local("lib.r") @@ -24,7 +24,7 @@ # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") -args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects +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") @@ -32,7 +32,7 @@ # ----- PROCESSING INFILE ----- cat("\tARGUMENTS PROCESSING INFO\n") -#saving the specific parameters +# saving the specific parameters method <- args$method if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute @@ -47,7 +47,7 @@ # ----- ARGUMENTS PROCESSING ----- cat("\tINFILE PROCESSING INFO\n") -#image is an .RData file necessary to use xset variable given by previous tools +# image is an .RData file necessary to use xset variable given by previous tools load(args$image) 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.*") @@ -83,7 +83,7 @@ getPlotChromPeakDensity(xdata, param = groupChromPeaksParam) if (exists("intval")) { - getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") + getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") } cat("\n\n") @@ -100,8 +100,8 @@ print(xset) 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") +# 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") cat("\n\n")