comparison xcms_xcmsSet.r @ 33:c363b9f1caef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

32:2bf1cb023c94

    BPPARAM <- MulticoreParam(args$BPPARAM); args$BPPARAM <- NULL
}
register(BPPARAM)

#saving the specific parameters
method <- args$method; args$method <- NULL

cat("\n\n")

# ----- INFILE PROCESSING -----

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)

33:c363b9f1caef

    BPPARAM <- MulticoreParam(args$BPPARAM); args$BPPARAM <- NULL
}
register(BPPARAM)

#saving the specific parameters
if (!is.null(args$filterAcquisitionNum)){
    filterAcquisitionNumParam <- args$filterAcquisitionNum; args$filterAcquisitionNum <- NULL
}
if (!is.null(args$filterRt)){
    filterRtParam <- args$filterRt; args$filterRt <- NULL
}
if (!is.null(args$filterMz)){
    filterMzParam <- args$filterMz; args$filterMz <- NULL
}

method <- args$method; args$method <- NULL

cat("\n\n")

# ----- INFILE PROCESSING -----

print(pd)

cat("\t\t\tLoad Raw Data\n")
raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk")

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)
}

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)

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)