# HG changeset patch
# User greg
# Date 1538750819 14400
# Node ID 8e6837a663512904a11de1f53785b8d1e4ef528e
# Parent  5f30220af0cdb8b443464884feaf807511badf3f
Uploaded

diff -r 5f30220af0cd -r 8e6837a66351 affy2vcf.xml
--- a/affy2vcf.xml	Thu Oct 04 10:34:37 2018 -0400
+++ b/affy2vcf.xml	Fri Oct 05 10:46:59 2018 -0400
@@ -7,7 +7,7 @@
 #set text_outputs_dir = 'text_outputs'
 mkdir $text_outputs_dir &&
 bcftools +affy2vcf.so
--- fasta_ref '$fasta_ref'
+--fasta_ref '$reference_genome.fasta_ref'
 --annot '$annot'
 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
 --summary '$text_outputs_dir/summary.txt'
@@ -26,15 +26,26 @@
     ]]></command>
     <inputs>
         <param name="annot" type="data" format="csv" label="Probeset annotation file" />
-        <param name="fasta_ref" 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"/>
-                <filter type="sort_by" column="1"/>
-                <validator type="no_options" message="No Fasta genome references are available.  Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/>
-            </options>
-        </param>
+        <conditional name="reference_genome">
+            <param name="source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
+                <option value="history" selected="true">Use a reference genome from my history</option>
+                <option value="cached">Use a locally cached genome index</option>
+            </param>
+            <when value="history">
+                <param name="fasta_ref" type="data" format="fasta" label="Select reference genome" />
+            </when>
+            <when value="cached">
+                <param name="fasta_ref" 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"/>
+                        <filter type="sort_by" column="1"/>
+                        <validator type="no_options" message="No cached Fasta genome references are available." />
+                    </options>
+                </param>
+            </when>
+        </conditional>
         <conditional name="output_gender_estimate_cond">
             <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
                 <option value="no" selected="true">No</option>