comparison anticipated_purity_dims.R @ 1:3f1f2d545f3a draft

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

0:4b417094bf71

  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,]
  }

1:3f1f2d545f3a

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