diff xcms_merge.r @ 11:67ab853b89f3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

--- a/xcms_merge.r	Thu Mar 08 05:52:52 2018 -0500
+++ b/xcms_merge.r	Tue Apr 03 11:38:21 2018 -0400
@@ -13,58 +13,11 @@
 
 cat("\tXSET MERGING...\n")
 
-for(image in args$images) {
-    load(image)
-    print(args)
-    # Handle infiles
-    if (!exists("singlefile")) singlefile <- NULL
-    if (!exists("zipfile")) zipfile <- NULL
-    rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
-    zipfile <- rawFilePath$zipfile
-    singlefile <- rawFilePath$singlefile
-    directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
-
-    if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
-    cat(sampleNamesList$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)
-    }
-}
+mergeXDataReturn <- mergeXData(args)
+xdata <- mergeXDataReturn$xdata
+singlefile <- mergeXDataReturn$singlefile
+md5sumList <- mergeXDataReturn$md5sumList
+sampleNamesList <- mergeXDataReturn$sampleNamesList
 
 # Create a sampleMetada file
 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")