comparison metaMS_runGC.r @ 7:89af36e05548 draft

planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit eb45457830f9d220bcb845acf71bffb50038a4c7

6:286ebb9f6e84

source_local <- function(fname) {
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}

pkgs <- c("metaMS","stringr","batch","CAMERA") #"batch" necessary for parseCommandArgs function
loadAndDisplayPackages(pkgs)


cat("\n\n")

modNamC <- "metaMS:runGC" ## module name
cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")

# ----- PROCESSING INFILE -----
cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
#write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')

    nSlaves=args$nSlaves
}

if (args$settings=="User_defined") {
    cat("Using user's parameters\n")
    fwhmparam=args$fwhm
    rtdiffparam=args$rtdiff
    minfeatparam=args$minfeat
    simthreshparam=args$simthreshold
    minclassfractionparam=args$minclassfraction
    minclasssizeparam=args$minclasssize

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

#peakTable for PCA 
#dataMatrix
cat("\nGenerating dataMatrix file")
dataMatrix<-cbind(Name=peaktable[,"Name"],peaktable[,(colnames(peaktable) %in% sampleMetadata[,1])])
rownames(dataMatrix)<-NULL
print(dataMatrix)
cat("\t.\t.")
write.table(dataMatrix, file="dataMatrix.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

#variableMetadata
cat("\nGenerating variableMetadata file")
print(colnames(peaktable))
variableMetadata<-peaktable[,!(colnames(peaktable) %in% sampleMetadata[,1])]
rownames(variableMetadata)<-NULL
cat("\t.")
write.table(variableMetadata, file="variableMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

write.table(sampleMetadata, file="sampleMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

#peak spectrum as MSP for DB search
cat("\nGenerating",length(resGC$PseudoSpectra),"peakspectra in peakspectra.msp file\n")
if(is.null(resGC$PseudoSpectra)){
    write("No results", file="peakspectra.msp")
}else{
    write.msp(resGC$PseudoSpectra, file="peakspectra.msp", newFile = TRUE)
}

#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 = "")

7:89af36e05548

source_local <- function(fname) {
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}
source_local("lib_metams.r")

pkgs <- c("metaMS","stringr","batch","CAMERA") #"batch" necessary for parseCommandArgs function
loadAndDisplayPackages(pkgs)

cat("\n\n")

modNamC <- "metaMS:runGC" ## module name
cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")


# ----- PROCESSING INFILE -----
cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
#write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')

    nSlaves=args$nSlaves
}

if (args$settings=="User_defined") {
    cat("Using user's parameters\n")
    rtdiffparam=args$rtdiff
    minfeatparam=args$minfeat
    simthreshparam=args$simthreshold
    minclassfractionparam=args$minclassfraction
    minclasssizeparam=args$minclasssize

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

#peakTable for PCA 
#dataMatrix
cat("\nGenerating dataMatrix file")
dataMatrix<-cbind(Name=peaktable[,"Name"],peaktable[,(colnames(peaktable) %in% sampleMetadata[,1])])
rownames(dataMatrix)<-NULL
cat("\t.\t.")
write.table(dataMatrix, file="dataMatrix.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

#variableMetadata
cat("\nGenerating variableMetadata file")
variableMetadata<-peaktable[,!(colnames(peaktable) %in% sampleMetadata[,1])]
rownames(variableMetadata)<-NULL
cat("\t.")
write.table(variableMetadata, file="variableMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

write.table(sampleMetadata, file="sampleMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)
cat("\t.\tOK")

#peak spectrum as MSP for DB search
cat("\nGenerating",length(resGC$PseudoSpectra),"peakspectra in peakspectra.msp file\n")
write.msp(resGC$PseudoSpectra, file="peakspectra.msp", newFile = TRUE)

#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"))
}