typo in help

bin/PEGASAS

@@ -48,13 +48,13 @@ def get_arg_parser():
 
 
 def add_pathway_parser( subparsers ):
-	arg_formatting = subparsers.add_parser("pathway", help='Calculates signaling pathway activaty derived from geneset enrichment metric based on RNA-Seq gene expression')
+	arg_formatting = subparsers.add_parser("pathway", help='Calculates signaling pathway activity derived from geneset enrichment metric based on RNA-Seq gene expression')
 	optional_args = arg_formatting._action_groups.pop()
 	required_args = arg_formatting.add_argument_group('required arguments')
 	required_args.add_argument('geneExpbySample',help='A TSV format matrix of gene expression values (FPKM, TPM, etc.) where each column is one sample and each row is one gene.')
 	required_args.add_argument('geneSignatureList',default=config.HALLMARKS50,help='One or multiple gene signature sets of pathway of interest in the format of \'gmt\' (see MSigDB webset).')
 	required_args.add_argument('groupInfo',help='A TSV format file provides patient ID and phenotype/disease stage in each row.')
-	optional_args.add_argument('-o','--out-dir', default='PEGASAS_PathwayScore', help='Output folder name of the analysis.')
+	optional_args.add_argument('-o','--out-dir', default='PEGASAS_pathway', help='Output folder name of the analysis.')
 	optional_args.add_argument('-n','--num-interval',default=40, help='Number of KS enrichment calculation processes one time.')
 	optional_args.add_argument('--plotting',default=False, action='store_true', help='Making plots to inspect K-S enrichment scores.')
 	arg_formatting._action_groups.append(optional_args)