Mercurial > repos > greg > affy2vcf

changeset 3:6274184a8b84 draft default tip

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Uploaded
author greg
date Fri, 30 Nov 2018 08:23:05 -0500
parents 02025c366fca
children
files affy2vcf.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/affy2vcf.xml	Thu Nov 01 09:11:57 2018 -0400
+++ b/affy2vcf.xml	Fri Nov 30 08:23:05 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>