Mercurial > repos > greg > assembly_post_processor

diff assembly_post_processor.xml @ 41:61977f3f19ea draft

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Uploaded
author greg
date Thu, 27 Apr 2017 10:23:48 -0400
parents b0ea1e985a38
children 3227f0f39800
line wrap: on
line diff
--- 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