# HG changeset patch
# User greg
# Date 1487255208 18000
# Node ID 29530d7a2a3df738b6e8cbede1e3541576afae1f
# Parent  963f84101cdc8f23086152111e057beebb228b28
Uploaded

diff -r 963f84101cdc -r 29530d7a2a3d phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Feb 15 07:59:49 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Feb 16 09:26:48 2017 -0500
@@ -72,6 +72,7 @@
                 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
                 --orthogroup_fna
             #end if
+            --config_dir '$scaffold.fields.path'
             --scaffold '$scaffold.fields.path'
             --method $method
 
@@ -97,9 +98,8 @@
                         #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                         #if str($rooting_order_file) == 'yes':
                             --rooting_order '$rooting_order_file_cond.rooting_order'
-                        #else:
-                            #set default_rooting_order = $os.path.join($__tool_directory__, 'rooting_order.config')
-                            --rooting_order '$default_rooting_order'
+			    # Noe else block needed here because the default rooting_order
+			    # configuration will be used if the --rooting_order flag is missing.
                         #end if
                         --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
                     #end if