diff xcms_xcmsSet.r @ 15:b62808a2a008 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_xcmsSet.r	Tue Sep 18 16:07:36 2018 -0400
@@ -0,0 +1,132 @@
+#!/usr/bin/env Rscript
+
+# ----- LOG FILE -----
+log_file <- file("log.txt", open="wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+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("lib.r")
+source_local("lib-xcms3.x.x.r")
+
+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')
+
+cat("\n\n")
+
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the commun parameters
+BPPARAM <- MulticoreParam(1)
+if (!is.null(args$BPPARAM)){
+    BPPARAM <- MulticoreParam(args$BPPARAM)
+}
+register(BPPARAM)
+
+#saving the specific parameters
+if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
+if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
+if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
+
+method <- args$method
+
+if (!is.null(args$roiList)){
+    cat("\t\troiList provided\n")
+    args$roiList <- list(getDataFrameFromFile(args$roiList))
+    print(args$roiList)
+}
+
+cat("\n\n")
+
+# ----- INFILE PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+## Get the full path to the files
+files <- getMSFiles(directory)
+
+cat("\t\t\tApply filter[s] (if asked)\n")
+if (exists("filterAcquisitionNumParam"))  raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
+if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
+if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
+#Apply this filter only if file contain MS and MSn
+if(length(unique(msLevel(raw_data)))!= 1){
+	raw_data <- filterMsLevel(raw_data,msLevel=1)
+}
+
+cat("\t\t\tChromatographic peak detection\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()))]
+
+findChromPeaksParam <- do.call(paste0(method,"Param"), args)
+print(findChromPeaksParam)
+xdata <- findChromPeaks(raw_data, param=findChromPeaksParam)
+
+# Check if there are no peaks
+if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
+
+# Transform the files absolute pathways into relative pathways
+xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
+
+# Create a sampleMetada file
+sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
+
+cat("\t\t\tCompute and Store TIC and BPI\n")
+chromTIC = chromatogram(xdata, aggregationFun = "sum")
+chromBPI = chromatogram(xdata, aggregationFun = "max")
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+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")
+save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
+
+
+cat("\tDONE\n")