comparison anticipated_purity_dims.R @ 8:f6996ad60d8f draft

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

7:d7f4696a1f86

  df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
  filename = NA
}else{
  indf <- read.table(opt$peaks_file,
                     header = TRUE, sep='\t', stringsAsFactors = FALSE)

  filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
  # check if the data file is mzML or RAW (can only use mzML currently) so
  # we expect an mzML file of the same name in the same folder
  indf$i <- indf[,colnames(indf)==filename]
  indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])

  filename = sub("raw", "mzML", filename, ignore.case = TRUE)

  df <- indf[4:nrow(indf),]
  if ('blank_flag' %in% colnames(df)){
    df <- df[df$blank_flag==1,]
  }

  colnames(df)[colnames(df)=='m.z'] <- 'mz'

  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{
    mzml_file <- file.path(opt$mzML_file, filename)
  }
}else{
  mzml_file <- opt$mzML_file
}

    iwNormFun = msPurity::iwNormQE.5()
}

print('FIRST ROWS OF PEAK FILE')
print(head(df))

predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                     filepth=mzml_file,
                                     minOffset=minOffset,
                                     maxOffset=maxOffset,
                                     ppm=opt$ppm,

8:f6996ad60d8f

  df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
  filename = NA
}else{
  indf <- read.table(opt$peaks_file,
                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
	
  filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
  print(filename)
  # check if the data file is mzML or RAW (can only use mzML currently) so
  # we expect an mzML file of the same name in the same folder
  indf$i <- indf[,colnames(indf)==filename]
  indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])

  filename = sub("raw", "mzML", filename, ignore.case = TRUE)
  print(filename)
  df <- indf[3:nrow(indf),]
  if ('blank_flag' %in% colnames(df)){
    df <- df[df$blank_flag==1,]
  }

  colnames(df)[colnames(df)=='m.z'] <- 'mz'

  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
}

    iwNormFun = msPurity::iwNormQE.5()
}

print('FIRST ROWS OF PEAK FILE')
print(head(df))
print(mzml_file)
predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                     filepth=mzml_file,
                                     minOffset=minOffset,
                                     maxOffset=maxOffset,
                                     ppm=opt$ppm,