docs: def run_compare_gold_standard(in_prefix, in_type, out_prefix, base_dir,
                                options):
      """Compares with a gold standard data set (compare_gold_standard.
  
      :param in_prefix: the prefix of the input files.
      :param in_type: the type of the input files.
      :param out_prefix: the output prefix.
      :param base_dir: the output directory.
      :param options: the options needed.
  
      :type in_prefix: str
      :type in_type: str
      :type out_prefix: str
      :type base_dir: str
      :type options: list
  
      :returns: a tuple containing the prefix of the output files (the input
                prefix for the next script) and the type of the output files
                (``bfile``).
  
      This function calls the :py:mod:`pyGenClean.Misc.compare_gold_standard`
      module. The required file type for this module is ``bfile``, hence the need
      to use the :py:func:`check_input_files` to check if the file input file
      type is the good one, or to create it if needed.
  
      .. note::
          The :py:mod:`pyGenClean.Misc.compare_gold_standard` module doesn't
          return usable output files. Hence, this function returns the input file
          prefix and its type.
  
      """
      # Creating the output directory
      os.mkdir(out_prefix)
  
      # We know we need bfile
      required_type = "bfile"
      check_input_files(in_prefix, in_type, required_type)
  
      # We need to inject the name of the input file and the name of the output
      # prefix
      script_prefix = os.path.join(out_prefix, "compare_with_gold")
      options += ["--{}".format(required_type), in_prefix,
                  "--out", script_prefix]
  
      # We run the script
      try:
          compare_gold_standard.main(options)
      except compare_gold_standard.ProgramError as e:
          msg = "compare_gold_standard: {}".format(e)
          raise ProgramError(msg)
  
      # We create the LaTeX summary
      latex_file = os.path.join(script_prefix + ".summary.tex")
      try:
          with open(latex_file, "w") as o_file:
              print >>o_file, latex_template.subsection(
                  compare_gold_standard.pretty_name
              )
  
      except IOError:
          msg = "{}: cannot write LaTeX summary".format(latex_file)
          raise ProgramError(msg)
  
      # We know this step doesn't produce an new data set, so we return the old
      # prefix and the old in_type
      return _StepResult(
          next_file=in_prefix,
          next_file_type=required_type,
          latex_summary=latex_file,
          description=compare_gold_standard.desc,
          long_description=compare_gold_standard.long_desc,
          graph_path=None,
      )