diff xcms_merge.r @ 7:dca722aecb67 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_merge.r	Thu Mar 01 04:15:19 2018 -0500
@@ -0,0 +1,83 @@
+#!/usr/bin/env Rscript
+
+#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");
+
+args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+
+# 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$args
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+cat("\tXSET MERGING...\n")
+
+for(image in args$images) {
+    load(image)
+    cat(sampleNamesList$sampleNamesOrigin,"\n")
+    if (!exists("xdata_merged")) {
+        xdata_merged <- xdata
+        singlefile_merged <- singlefile
+        md5sumList_merged <- md5sumList
+        sampleNamesList_merged <- sampleNamesList
+    } else {
+        xdata_merged <- c(xdata_merged,xdata)
+        singlefile_merged <- c(singlefile_merged,singlefile)
+        md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
+        sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
+        sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
+    }
+}
+rm(image)
+xdata <- xdata_merged; rm(xdata_merged)
+singlefile <- singlefile_merged; rm(singlefile_merged)
+md5sumList <- md5sumList_merged; rm(md5sumList_merged)
+sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
+
+if (!is.null(args$sampleMetadata)) {
+    cat("\tXSET PHENODATA SETTING...\n")
+    sampleMetadataFile <- args$sampleMetadata
+    sampleMetadata <- read.table(sampleMetadataFile, h=F, sep=";", stringsAsFactors=F)
+    if (ncol(sampleMetadata) < 2) sampleMetadata <- read.table(sampleMetadataFile, h=F, sep="\t", stringsAsFactors=F)
+    if (ncol(sampleMetadata) < 2) sampleMetadata <- read.table(sampleMetadataFile, h=F, sep=",", stringsAsFactors=F)
+    if (ncol(sampleMetadata) < 2) {
+        error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
+        print(error_message)
+        stop(error_message)
+    }
+    xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
+
+    if (any(is.na(pData(xdata)$sample_group))) {
+        sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
+        error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
+        print(error_message)
+        stop(error_message)
+    }
+}
+save.image()
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(pData(xdata))
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+print(xset@phenoData)
+print(xset)
+cat("\n\n")
+
+cat("\tSAVE RData\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="merged.RData")