comparison metaMS_runGC.r @ 5:b8d4129dd2a6 draft

planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit c7a518686137f6d62b7415715152e8d5a9953ed7

4:c10824185547

cat("\t\tCOMPUTE\n\n")

#runGC accept either a list of files a zip folder or an xset object from xcms.xcmsSet tool
#From xset is an .RData file necessary to use the xcmsSet object generated by xcms.xcmsSet given by previous tools
if (!is.null(args$singlefile_galaxyPath)){
    cat("Loading datas from XCMS file(s)...\n")
    load(args$singlefile_galaxyPath)
    
    #Transform XCMS object if needed
    if(!exists("xset")) {
        if(exists("xdata")) {

        } else {
            error_message="no xset and no xdata... Probably a problem"
            print(error_message)
            stop(error_message)
        }
    }

    #xset from xcms.xcmsSet is not well formatted for metaMS this function do the formatting
    if (class(xset)=="xcmsSet"){
        if (length(xset@rt$raw)>1){

            xsetCAM <- xset.l
        }
        
        #default settings for GC from Wehrens et al
        cat("Process runGC with metaMS package...\n\n")
        print(str(TSQXLS.GC))  
        resGC<-runGC(xset=xsetCAM,settings=TSQXLS.GC, rtrange=rtrange, DB= DBgc, removeArtefacts = TRUE, 
                    findUnknowns = TRUE, returnXset = TRUE, RIstandards = RIarg, nSlaves = nSlaves)
    } else {
        if(args$settings == "User_defined") {
            settingslist=GALAXY.GC

#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("resGC", "xset", "singlefile", "zipfile", "DBgc")
save(list = objects2save[objects2save %in% ls()], file = "runGC.RData")

cat("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "")

5:b8d4129dd2a6

cat("\t\tCOMPUTE\n\n")

#runGC accept either a list of files a zip folder or an xset object from xcms.xcmsSet tool
#From xset is an .RData file necessary to use the xcmsSet object generated by xcms.xcmsSet given by previous tools
if (!is.null(args$singlefile_galaxyPath)){
    cat("Loading datas from XCMS files...\n")
    load(args$singlefile_galaxyPath)
    
    #Transform XCMS object if needed
    if(!exists("xset")) {
        if(exists("xdata")) {

        } else {
            error_message="no xset and no xdata... Probably a problem"
            print(error_message)
            stop(error_message)
        }
    }
    #Verify that there are more than 1 file (can't run metaMS on only 1 file)
    if(length(rownames(xdata@phenoData)) < 2){
        error_message="You need more than 1 file to be able to run metaMS"
        print(error_message)
        stop(error_message)
    }

    #xset from xcms.xcmsSet is not well formatted for metaMS this function do the formatting
    if (class(xset)=="xcmsSet"){
        if (length(xset@rt$raw)>1){

            xsetCAM <- xset.l
        }
        
        #default settings for GC from Wehrens et al
        cat("Process runGC with metaMS package...\n\n")
        print(str(TSQXLS.GC))
        resGC<-runGC(xset=xsetCAM,settings=TSQXLS.GC, rtrange=rtrange, DB= DBgc, removeArtefacts = TRUE, 
                    findUnknowns = TRUE, returnXset = TRUE, RIstandards = RIarg, nSlaves = nSlaves)
    } else {
        if(args$settings == "User_defined") {
            settingslist=GALAXY.GC

#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("resGC", "xset", "singlefile", "zipfile", "DBgc")
save(list = objects2save[objects2save %in% ls()], file = "runGC.RData")

cat("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "")

#WARNING if user has CDF files (not yet good for plotting)
files <- paste("./",names(singlefile),sep="")
if(MSnbase:::isCdfFile(files)){
    warning_message <- "You have CDF files, for the moment you can't obtain plot after runGC! A new update will follow with the good correction"
    warning(warning_message)
    cat(paste("\n","/!\\Warning/!\\",warning_message,sep="\n"))
}