comparison xcms_fillpeaks.r @ 44:1b5fb5a27f5e draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"

43:eeade1310758

if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")

# 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 -----

fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
print(fillChromPeaksParam)

# back compatibility between xcms-3.0.0 and xcms-3.5.2
xdata <- updateObject(xdata)

xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)

if (exists("intval")) {
    getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
}

44:1b5fb5a27f5e

if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")

# Handle infiles
if (!exists("singlefile")) singlefile <- NULL
if (!exists("zipfile")) zipfile <- NULL
rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
zipfile <- rawFilePath$zipfile
singlefile <- rawFilePath$singlefile


cat("\n\n")

# ----- MAIN PROCESSING INFO -----

fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
print(fillChromPeaksParam)

# back compatibility between xcms-3.0.0 and xcms-3.5.2
xdata <- updateObject(xdata)
register(SerialParam())
xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)

if (exists("intval")) {
    getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
}