# HG changeset patch
# User greg
# Date 1491931096 14400
# Node ID f73151ec679b2399c7ce18af1da36196bf3463f3
# Parent  b78f5b0d08058014347dc29c055fb6773ab21b03
Uploaded

diff -r b78f5b0d0805 -r f73151ec679b gene_family_phylogeny_builder.py
--- a/gene_family_phylogeny_builder.py	Tue Apr 11 13:13:53 2017 -0400
+++ b/gene_family_phylogeny_builder.py	Tue Apr 11 13:18:16 2017 -0400
@@ -8,7 +8,7 @@
 
 parser = argparse.ArgumentParser()
 
-parser.add_argument('--alignments_type', dest='alignments_type', help='Input alignments type produced by the GeneFamilyAligner')
+parser.add_argument('--alignment_type', dest='alignment_type', help='Input alignments type produced by the GeneFamilyAligner')
 parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
 parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, help='Maximum number of sequences in orthogroup alignments')
@@ -27,7 +27,7 @@
 
 # Build the command line.
 cmd = 'GeneFamilyPhylogenyBuilder'
-cmd += ' --alignment_type %s' % args.tree_inference
+cmd += ' --alignment_type %s' % args.alignment_type
 if args.bootstrap_replicates is not None:
     cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
 cmd += ' --config_dir %s' % args.config_dir