# HG changeset patch
# User greg
# Date 1493303028 14400
# Node ID 61977f3f19eaf2f9a6723581fbbbcfc68905a6c3
# Parent  8102c8bf241401e0000f88b99e44ce2ff9a34f43
Uploaded

diff -r 8102c8bf2414 -r 61977f3f19ea assembly_post_processor.xml
--- a/assembly_post_processor.xml	Wed Apr 26 12:45:43 2017 -0400
+++ b/assembly_post_processor.xml	Thu Apr 27 10:23:48 2017 -0400
@@ -15,10 +15,11 @@
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
-                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
-                    --method '$options_type.target_gene_family_assembly_cond.method'
-                    --gap_trimming $options_type.gap_trimming
+                    #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
+                    --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
+                    --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
+                    --method '$target_gene_family_assembly_cond.method'
+                    --gap_trimming $target_gene_family_assembly_cond.gap_trimming
                 #end if
                 #if str($options_type.strand_specific) == 'yes':
                     --strand_specific