comparison xcms_fillpeaks.r @ 34:d8bac1291473 draft

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

33:ea611367e1da

cat("\tARGUMENTS PROCESSING INFO\n")

#saving the specific parameters
method <- "FillChromPeaks"

if (!is.null(args$convertRTMinute)){
    convertRTMinute <- args$convertRTMinute; args$convertRTMinute <- NULL
}
if (!is.null(args$numDigitsMZ)){
    numDigitsMZ <- args$numDigitsMZ; args$numDigitsMZ <- NULL
}
if (!is.null(args$numDigitsRT)){
    numDigitsRT <- args$numDigitsRT; args$numDigitsRT <- NULL
}
if (!is.null(args$intval)){
    intval <- args$intval; args$intval <- NULL
}

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image); args$image=NULL
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.*")

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

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)

# Check some character issues
md5sumList <- list("origin" = getMd5sum(directory))
checkXmlStructure(directory)

cat("\t\tCOMPUTE\n")

cat("\t\t\tFilling missing peaks using default settings\n")
fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
print(fillChromPeaksParam)
xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)

if (exists("intval")) {

34:d8bac1291473

cat("\tARGUMENTS PROCESSING INFO\n")

#saving the specific parameters
method <- "FillChromPeaks"

if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
if (!is.null(args$intval)) intval <- args$intval

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image)
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.*")

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

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)

cat("\t\tCOMPUTE\n")

cat("\t\t\tFilling missing peaks using default settings\n")
# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]

fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
print(fillChromPeaksParam)
xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)

if (exists("intval")) {