# HG changeset patch
# User greg
# Date 1488385017 18000
# Node ID 7fc692c81c0293bff9b86c36795f03445404be2a
# Parent  bbc153dbaee75afb3cca7c2beebb1bc25989e5de
Uploaded

diff -r bbc153dbaee7 -r 7fc692c81c02 kaks_analysis.xml
--- a/kaks_analysis.xml	Wed Mar 01 11:13:06 2017 -0500
+++ b/kaks_analysis.xml	Wed Mar 01 11:16:57 2017 -0500
@@ -13,6 +13,7 @@
     </stdio>
     <command>
         <![CDATA[
+            #set comparison = $comparison_cond.comparison
             #if str($options_type.options_type_selector) == 'advanced':
                 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
                 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
@@ -25,7 +26,7 @@
             --coding_sequences_species_1 '$coding_sequences_species_1'
             --proteins_species_1 '$proteins_species_1'
             --comparison $comparison
-            #if str($comparison_cond.comparison) == 'orthologs':
+            #if str($comparison) == 'orthologs':
                 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
                 --proteins_species_2 '$comparison_cond.proteins_species_2'
             #end if