comparison anticipated_purity_dims.R @ 9:cc4464eb380f draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

8:f6996ad60d8f

  if ('nan' %in% df$mz){
    df[df$mz=='nan',]$mz <- NA
  }
  df$mz <- as.numeric(df$mz)




}

}else{
    isotopes <- TRUE
}


if (dir.exists(opt$mzML_file)){
  # if directory then we need to add a file name
  print(filename)
  if (is.na(filename)){
    print('ERROR: If a directory is provided then a filename needs to be entered
          directory or automatically obtained by using a dimspy output')
    quit()
  }else{
    print('filename derived from dimspy')
    mzml_file <- file.path(opt$mzML_file, filename)
  }
}else{
  mzml_file <- opt$mzML_file
}

if (is.null(opt$sim)){
    sim=FALSE
}else{
    sim=TRUE

9:cc4464eb380f

  if ('nan' %in% df$mz){
    df[df$mz=='nan',]$mz <- NA
  }
  df$mz <- as.numeric(df$mz)
  mzml_file <- file.path(opt$mzML_file, filename)	



}

}else{
    isotopes <- TRUE
}



if (is.null(opt$sim)){
    sim=FALSE
}else{
    sim=TRUE