comparison flagRemove.R @ 3:59c1f9077c3b draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db

2:054189c06bb1

  make_option("--temp_save",  action="store_true",
              help="Assign True if files for each step saved (for testing purposes) [default = %default]"
  ),

  make_option("--samplelist",  type="character", help="Sample list to determine the blank class"),

  make_option("--xset_name",  default="xset",
              help="Name of the xcmsSet object within the RData file [default = %default]"
  )



)

}


print(opt)

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

xset<-loadRData(opt$xset_path, opt$xset_name)
print(xset)
if (is.null(opt$samplelist)){
    blank_class <- opt$blank_class
}else{
    samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)

3:59c1f9077c3b

  make_option("--temp_save",  action="store_true",
              help="Assign True if files for each step saved (for testing purposes) [default = %default]"
  ),

  make_option("--samplelist",  type="character", help="Sample list to determine the blank class")





)

}


print(opt)

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)
    }
}


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]))
}

xset <- loadRData(opt$xset_path, c('xset','xdata'))

print(xset)
if (is.null(opt$samplelist)){
    blank_class <- opt$blank_class
}else{
    samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)