# HG changeset patch
# User greg
# Date 1543584158 18000
# Node ID 5b64c88d706f314e41c120dab1f1c67dbf0bfbc9
# Parent  640d50a570637a29ed7de513eebf6472f1bf7d6c
Uploaded

diff -r 640d50a57063 -r 5b64c88d706f affy2vcf.xml
--- a/affy2vcf.xml	Thu Nov 01 09:09:53 2018 -0400
+++ b/affy2vcf.xml	Fri Nov 30 08:22:38 2018 -0500
@@ -14,7 +14,7 @@
 #if str($reference_genome_source_cond.reference_genome_source) == "history":
     --fasta-ref '$reference_genome_source_cond.history_item'
 #else:
-    --fasta-ref '$reference_genome_source_cond.locally_cached_item'
+    --fasta-ref '$reference_genome_source_cond.locally_cached_item.fields.path'
 #end if
 --annot '$annot'
 --snp-posteriors '$snp_posteriors'
@@ -50,9 +50,9 @@
             <when value="cached">
                 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
                     <options from_data_table="all_fasta">
-                        <column name="name" index="1"/>
-                        <column name="value" index="2"/>
-                        <column name="path" index="2"/>
+                        <column name="name" index="2"/>
+                        <column name="value" index="0"/>
+                        <column name="path" index="3"/>
                         <filter type="sort_by" column="1"/>
                         <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
                     </options>