Mercurial > repos > greg > gene_family_classifier

changeset 21:795745116516 draft

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Uploaded
author greg
date Tue, 10 Jan 2017 10:33:47 -0500
parents 038777896b71
children 035e8b85cdf7
files gene_family_classifier.xml
diffstat 1 files changed, 15 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- 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