comparison frag4feature.R @ 5:faba6cd56875 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty

4:7e633c70fdfc

opt<- parse_args(OptionParser(option_list=option_list))

loadRData <- function(rdata_path, name){
#loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() == name]))
}

# Requires
pa <- loadRData(opt$pa, 'pa')
xset <- loadRData(opt$xset, 'xset')

pa@cores <- opt$cores

print(pa@fileList)
print(xset@filepaths)

pa <- fix[[1]]
xset <- fix[[2]]

if(is.null(opt$grp_peaklist)){
    grp_peaklist = NA


}else{
    grp_peaklist = opt$grp_peaklist
}

print('heck')

5:faba6cd56875

opt<- parse_args(OptionParser(option_list=option_list))

loadRData <- function(rdata_path, name){
#loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() %in% name]))
}

# This function retrieve a xset like object
#@author Gildas Le Corguille [e-mail]
getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet")
        return (xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
        sampclass(xset) <- xset@phenoData$sample_group
        return (xset)
    }
}

# Requires
pa <- loadRData(opt$pa, 'pa')
xset <- loadRData(opt$xset, c('xset','xdata'))
xset <- getxcmsSetObject(xset)

pa@cores <- opt$cores

print(pa@fileList)
print(xset@filepaths)

pa <- fix[[1]]
xset <- fix[[2]]

if(is.null(opt$grp_peaklist)){
    grp_peaklist = NA
}else{
    grp_peaklist = opt$grp_peaklist
}

print('heck')