diff xcms_xcmsSet.r @ 32:2bf1cb023c94 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_xcmsSet.r	Thu Mar 01 04:14:39 2018 -0500
@@ -0,0 +1,126 @@
+#!/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")
+
+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); args$BPPARAM <- NULL
+}
+register(BPPARAM)
+
+#saving the specific parameters
+method <- args$method; args$method <- NULL
+
+cat("\n\n")
+
+# ----- INFILE PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+args <- rawFilePath$args
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+# Check some character issues
+md5sumList <- list("origin" = getMd5sum(directory))
+checkXmlStructure(directory)
+checkFilesCompatibilityWithXcms(directory)
+
+
+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\tCreate a phenodata data.frame\n")
+s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1))
+s_name <- tools::file_path_sans_ext(basename(files))
+pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE)
+print(pd)
+
+cat("\t\t\tLoad Raw Data\n")
+raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk")
+
+cat("\t\t\tChromatographic peak detection\n")
+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)
+save.image()
+# Create a sampleMetada file
+sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
+
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+
+cat("\n\n")
+
+
+# -- TIC --
+cat("\t\tGET TIC GRAPH\n")
+#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
+getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
+getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+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")
+save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
+
+
+cat("\tDONE\n")