comparison xcms.r @ 21:beda2d981b9d draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312

20:a79d839d625f

#execution of the function "thefunction" with the parameters given in "listArguments"

cat("\t\tCOMPUTE\n")
xset = do.call(thefunction, listArguments)


cat("\n\n")

dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)

if (thefunction  == "xcmsSet") {

    #transform the files absolute pathways into relative pathways
    xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
    print(zipfile)
    if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {

        #Modify the samples names (erase the path)
        for(i in 1:length(sampnames(xset))){

21:beda2d981b9d

#execution of the function "thefunction" with the parameters given in "listArguments"

cat("\t\tCOMPUTE\n")
xset = do.call(thefunction, listArguments)

# check if there are no peaks
if (nrow(peaks(xset)) == 0) {
    stop("No peaks were detected. You should review your settings")
}


cat("\n\n")

dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)

if (thefunction  == "xcmsSet") {

    #transform the files absolute pathways into relative pathways
    xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
    if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {

        #Modify the samples names (erase the path)
        for(i in 1:length(sampnames(xset))){