# HG changeset patch
# User greg
# Date 1484150740 18000
# Node ID ec58d25386fcdd31f270230e9f80c4832051bc55
# Parent  7d0cc822c94ea6fe6071b20c1fb8865cc735ff38
Uploaded

diff -r 7d0cc822c94e -r ec58d25386fc phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Tue Jan 10 12:30:52 2017 -0500
+++ b/phylogenomics_analysis.xml	Wed Jan 11 11:05:40 2017 -0500
@@ -77,8 +77,15 @@
                     #if str($input_includes_coding_sequences) == 'yes':
                         #set multiple_codon_alignments_cond = $input_includes_coding_sequences_cond.multiple_codon_alignments_cond
                         #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
-                        #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
-                        #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
+                        #if str($input_includes_coding_sequences) == 'yes':
+                            #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
+                            #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
+                        #else:
+                            #set use_corresponding_coding_sequences = 'no'
+                        #end if
+                    #else:
+                        #set multiple_codon_alignments = 'no'
+                        #set use_corresponding_coding_sequences = 'no'
                     #end if
 
                     #if str($multiple_sequence_alignments_option) == 'create_alignments':