new_contents: #!/usr/bin/env python
  # coding: utf-8
  
  import pandas as pd
  import scIB
  import warnings
  warnings.filterwarnings('ignore')
  import argparse
  from functools import reduce
  
  if __name__=='__main__':
      """
      Scale LISI scores in the output of merge_metrics.py
      """
      
      parser = argparse.ArgumentParser(description='Scale LISI scores')
  
      parser.add_argument('-i', '--input', required=True, help='Merged metrics file in csv file format')
      parser.add_argument('-o', '--output', required=True, help='Merged and LISI-scaled metrics file in csv file format')
      
      args = parser.parse_args()
      
      #get input file
      file = args.input
      res = pd.read_csv(file, index_col=0)
      
      #select columns with LISI score and scale
     
      
      results = res.T
      #write output file
      results.to_csv(args.output)
  
subject: scale snakemake metrics output file - skeleton