# HG changeset patch
# User greg
# Date 1484062427 18000
# Node ID 795745116516840c443f6ded37f1edefb7dd42e4
# Parent  038777896b71fac61e70bea1ea24e62ee483c7bc
Uploaded

diff -r 038777896b71 -r 795745116516 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Jan 10 10:16:18 2017 -0500
+++ b/gene_family_classifier.xml	Tue Jan 10 10:33:47 2017 -0500
@@ -12,19 +12,26 @@
     </stdio>
     <command>
         <![CDATA[
-            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                #import os
-                #set create_ortho_sequences = True
-                #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
-                #set dest_dir = $output.extra_files_path
+            #if str($options_type.options_type_selector) == 'advanced':
                 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
                 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
-                #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
-                #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
-                    #set create_corresponding_coding_sequences = True
+                #if str($create_orthogroup) == 'yes':
+                    #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
+                    #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
+                        #set create_corresponding_coding_sequences = True
+                    #else:
+                        #set create_corresponding_coding_sequences = False
                 #else:
                     #set create_corresponding_coding_sequences = False
                 #end if
+                #if str($create_orthogroup) == 'yes':
+                    #import os
+                    #set create_ortho_sequences = True
+                    #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
+                    #set dest_dir = $output.extra_files_path
+                #else:
+                    #set create_ortho_sequences = False
+                #end if
                 mkdir -p $dest_dir &&
             #else:
                 #set create_ortho_sequences = False