# HG changeset patch
# User greg
# Date 1494612867 14400
# Node ID 2de4563e70cf18618a246ddd6cb901c4a90e4969
# Parent  3d78d366dfcc906e48401d06753b9c4d4705dcce
Uploaded

diff -r 3d78d366dfcc -r 2de4563e70cf gene_family_phylogeny_builder.py
--- a/gene_family_phylogeny_builder.py	Fri May 12 14:14:19 2017 -0400
+++ b/gene_family_phylogeny_builder.py	Fri May 12 14:14:27 2017 -0400
@@ -18,8 +18,8 @@
 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_tree', dest='output_tree', default=None, help='Output for phylogenetic trees')
+parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, 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')
@@ -52,6 +52,7 @@
     src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln')
     utils.move_directory_files(src_output_dir, args.output_phylip_dir)
     utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir)
-#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)
+if args.output_tree is not None and args.output_tree_dir is not None:
+    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
+    utils.move_directory_files(src_output_dir, args.output_tree_dir, copy=True)
+    utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)