comparison xcms.r @ 6:60f6c208ca16 draft

planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e

5:b9a87af62223

}




if (thefunction == "xcmsSet" || thefunction == "retcor") {
  ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
  bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
}

#necessary to unzip .zip file uploaded to Galaxy

    stop(error_message)
  }
}

# We unzip automatically the chromatograms from the zip files.
if (thefunction == "xcmsSet" || thefunction == "retcor" || thefunction == "fillPeaks")  {
  if(exists("zipfile") && (zipfile!="")) {
    if(!file.exists(zipfile)){
      error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
      print(error_message)
      stop(error_message)
    }

    #list all file in the zip file
    #zip_files=unzip(zipfile,list=T)[,"Name"]

    #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]
    if (length(directories) == 1) directory=directories else directory=".";

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

    # 
    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.

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("^.*/database/job_working_directory/[0123456789]+/[0123456789]+/" ,"", xset@filepaths)
  xset@filepaths<-sub("^.*/database/jobs/[0123456789]+/[0123456789]+/" ,"", xset@filepaths)
  if(exists("zipfile") && (zipfile!="")) {
    
    #Modify the samples names (erase the path)
    for(i in 1:length(sampnames(xset))){

6:60f6c208ca16

}




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

#necessary to unzip .zip file uploaded to Galaxy

    stop(error_message)
  }
}

# We unzip automatically the chromatograms from the zip files.
if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
  if(exists("zipfile") && (zipfile!="")) {
    if(!file.exists(zipfile)){
      error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
      print(error_message)
      stop(error_message)
    }

    #list all file in the zip file
    #zip_files=unzip(zipfile,list=T)[,"Name"]


    #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.

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