old_contents: #!/usr/bin/env python3
  import ursgal
  import os
  
  
  def main():
      """."""
      mzml = os.path.join(
          os.pardir,
          'example_data',
          'BSA1.mzML'
      )
  
      params = {
          'csv_filter_rules': [
              ['estimated_FDR', 'lte', 0.06],
              ['Is decoy', 'equals', 'false']
          ],
          'compress_raw_search_results_if_possible' : False,
          'database': os.path.join(
              os.pardir,
              'example_data',
              'BSA.fasta'
          )
      }
  
      engines = [
          'msgfplus_v9979'
      ]
  
      uc = ursgal.UController(
          profile='LTQ XL low res',
          params =params
      )
  
      mgf = uc.convert_to_mgf_and_update_rt_lookup(
          input_file=mzml
      )
      results = []
      for engine in engines:
          res = uc.search(
              input_file=mgf,
              engine=engine
          )
          val = uc.validate(
              input_file=res,
              engine='percolator_2_08'
          )
          fil = uc.filter_csv(
              input_file=val
          )
          results.append(file)
  
      quant = uc.execute_unode(
          input_file=mzml,
          engine='pyQms_0_0_1'
      )
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python3
  import ursgal
  import os
  
  
  def main():
      """."""
      mzml = os.path.join(
          os.pardir,
          'example_data',
          'search_with_label_15N',
          'JB_FASP_pH8_2-3_28122012.mzML'
      )
  
      params = {
          'csv_filter_rules': [
              ['estimated_FDR', 'lte', 0.06],
              ['Is decoy', 'equals', 'false']
          ],
          'compress_raw_search_results_if_possible' : False,
          'database': os.path.join(
              os.pardir,
              'example_data',
              'Creinhardtii_281_v5_5_CP_MT_with_contaminants_target_decoy.fasta'
          )
      }
  
      engines = [
          'msgfplus_v9979'
      ]
  
      uc = ursgal.UController(
          profile='LTQ XL low res',
          params =params
      )
  
      mgf = uc.convert_to_mgf_and_update_rt_lookup(
          input_file=mzml
      )
      results = []
      for engine in engines:
          res = uc.search(
              input_file=mgf,
              engine=engine
          )
          val = uc.validate(
              input_file=res,
              engine='percolator_2_08'
          )
          fil = uc.filter_csv(
              input_file=val
          )
          results.append(file)
  
      quant = uc.execute_unode(
          input_file=mzml,
          engine='pyQms_0_0_1'
      )
  
  if __name__ == '__main__':
      main()
  
subject: fix in example script