diff msnbase_readmsdata.r @ 0:728ebc7ae7dd draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msnbase_readmsdata.r	Tue Sep 18 16:04:51 2018 -0400
@@ -0,0 +1,99 @@
+#!/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("MSnbase","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")
+
+
+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
+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")
+
+# Transform the files absolute pathways into relative pathways
+raw_data@processingData@files <- sub(paste(getwd(), "/", sep="") , "", raw_data@processingData@files)
+
+# Create a sampleMetada file
+sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv")
+
+cat("\t\t\tCompute and Store TIC and BPI\n")
+chromTIC <- chromatogram(raw_data, aggregationFun = "sum")
+chromBPI <- chromatogram(raw_data, aggregationFun = "max")
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tMSnExp OBJECT INFO\n")
+print(raw_data)
+cat("\t\tphenoData\n")
+print(raw_data@phenoData@data)
+cat("\n\n")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
+save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData")
+
+
+cat("\tDONE\n")