--- a/gene_family_phylogeny_builder.py	Thu May 11 13:42:24 2017 -0400
+++ b/gene_family_phylogeny_builder.py	Thu May 11 13:42:33 2017 -0400
@@ -16,10 +16,10 @@
 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
 parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path')
-parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
-parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path')
-parser.add_argument('--output_tree', dest='output_tree', help='Output for phylogenetic trees')
-parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path')
+#parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
+#parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path')
+#parser.add_argument('--output_tree', dest='output_tree', help='Output for phylogenetic trees')
+#parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path')
 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference')
@@ -48,6 +48,7 @@
 utils.run_command(cmd)
 
 # Handle outputs.
+"""
 if args.output_phylip is not None and args.output_phylip_dir is not None:
     src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln')
     utils.move_directory_files(src_output_dir, args.output_phylip_dir)
@@ -55,3 +56,4 @@
 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
 utils.move_directory_files(src_output_dir, args.output_tree_dir)
 utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)
+"""