comparison xcms.r @ 15:1c78d61fd646 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093

14:8a23c743e6ea

for(pkg in pkgs) {
  suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
  cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
}
source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
cat("\n\n"); 

xsetRdataOutput = paste(thefunction,"RData",sep=".")
if (!is.null(listArguments[["xsetRdataOutput"]])){
  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
}

rplotspdf = "Rplots.pdf"
if (!is.null(listArguments[["rplotspdf"]])){
  rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
}

sampleMetadataOutput = "sampleMetadata.tsv"
if (!is.null(listArguments[["sampleMetadataOutput"]])){
  sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
}




if (thefunction %in% c("xcmsSet","retcor")) {
  ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
  bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
}

    #unzip
    suppressWarnings(unzip(zipfile, unzip="unzip"))

    #get the directory name
    filesInZip=unzip(zipfile, list=T); 
    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
    directory = "."
    if (length(directories) == 1) directory = directories
    
    cat("files_root_directory\t",directory,"\n")

    # 
    md5sumList=list("origin"=getMd5sum(directory))

    # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
    # Remove because can create issue with some clean files
    #@TODO: fix me

#     par(xpd=T, mar=par()$mar+c(0,0,0,4))
#}


#execution of the function "thefunction" with the parameters given in "listArguments"
xset = do.call(thefunction, listArguments)


cat("\n\n")

  #transform the files absolute pathways into relative pathways
  xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)

  if(exists("zipfile") && (zipfile!="")) {
    
    #Modify the samples names (erase the path)
    for(i in 1:length(sampnames(xset))){

      sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
      sample_name=sample_name[length(sample_name)]

}

# -- TIC --
if (thefunction == "xcmsSet") {
  sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
  getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
} else if (thefunction == "retcor") {
  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
  getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
}

cat("\n\n")


# ----- EXPORT -----

cat("\tXSET OBJECT INFO\n")
print(xset)

cat("\n\n")


cat("\tDONE\n")

15:1c78d61fd646

for(pkg in pkgs) {
  suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
  cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
}
source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
cat("\n\n");

xsetRdataOutput = paste(thefunction,"RData",sep=".")
if (!is.null(listArguments[["xsetRdataOutput"]])){
  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
}

#saving the specific parameters
rplotspdf = "Rplots.pdf"
if (!is.null(listArguments[["rplotspdf"]])){
  rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
}
sampleMetadataOutput = "sampleMetadata.tsv"
if (!is.null(listArguments[["sampleMetadataOutput"]])){
  sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
}
variableMetadataOutput = "variableMetadata.tsv"
if (!is.null(listArguments[["variableMetadataOutput"]])){
  variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
}
dataMatrixOutput = "dataMatrix.tsv"
if (!is.null(listArguments[["dataMatrixOutput"]])){
  dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
}
if (!is.null(listArguments[["convertRTMinute"]])){
  convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
}
if (!is.null(listArguments[["numDigitsMZ"]])){
  numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL
}
if (!is.null(listArguments[["numDigitsRT"]])){
  numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
}
if (!is.null(listArguments[["intval"]])){
  intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
}

if (thefunction %in% c("xcmsSet","retcor")) {
  ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
  bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
}

    #unzip
    suppressWarnings(unzip(zipfile, unzip="unzip"))

    #get the directory name
    filesInZip=unzip(zipfile, list=T);
    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
    directory = "."
    if (length(directories) == 1) directory = directories

    cat("files_root_directory\t",directory,"\n")

    #
    md5sumList=list("origin"=getMd5sum(directory))

    # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
    # Remove because can create issue with some clean files
    #@TODO: fix me

#     par(xpd=T, mar=par()$mar+c(0,0,0,4))
#}


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

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


cat("\n\n")

  #transform the files absolute pathways into relative pathways
  xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)

  if(exists("zipfile") && (zipfile!="")) {

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

      sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
      sample_name=sample_name[length(sample_name)]

}

# -- TIC --
if (thefunction == "xcmsSet") {
  cat("\t\tGET TIC GRAPH\n")
  sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
  getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
} else if (thefunction == "retcor") {
  cat("\t\tGET TIC GRAPH\n")
  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
  getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
}

if (thefunction == "fillPeaks") {
  cat("\t\tGET THE PEAK LIST\n")
  getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
}


cat("\n\n")

# ----- EXPORT -----

cat("\tXSET OBJECT INFO\n")
print(xset)

cat("\n\n")


cat("\tDONE\n")