Change organism type parameter from boolean to string type.

scripts/run_targetp.py

@@ -8,10 +8,10 @@ targetp_tool = config.load_config()['tools'].get('targetp', 'targetp')
 
 parser = argparse.ArgumentParser(description = 'Determine subcellular locations of eukaryotic amino acid sequences')
 parser.add_argument('--fasta', '-f', required = True, help = 'A fasta file with amino acid sequences')
-parser.add_argument('--plant', '-p', action = 'store_true', help = 'Wether sequences originate from plants')
+parser.add_argument('--organism_group', choices = ['plant', 'non-plant'], required = True, help = 'Define wether to use plant/non-plant networks')
 parser.add_argument('--output', required = True, help = 'The output file')
 args = parser.parse_args()
 
-plant_flag = '-P' if args.plant else '-N'
+org_flags = {'plant': '-P', 'non-plant': '-N'}
 
-system(targetp_tool + " " + plant_flag + " " + args.fasta + " > " + args.output)
+system(targetp_tool + " " + org_flags[args.organism_group]  + " " + args.fasta + " > " + args.output)