# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1373092134 18000
# Node ID a718ecb27e02df7b7546f0ed3ed1b8dc1d9a5092
# Parent  ea76da1e72813402d209af67fda07da9bd4787ef
Comment out getting reference from history, need wrapper for that

diff -r ea76da1e7281 -r a718ecb27e02 shear_sv.xml
--- a/shear_sv.xml	Fri Jul 05 15:22:04 2013 -0400
+++ b/shear_sv.xml	Sat Jul 06 01:28:54 2013 -0500
@@ -29,35 +29,43 @@
     <conditional name="genomeSource">
       <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
         <option value="indexed" selected="true">Use a cached reference genome</option>
+        <!--
         <option value="history">Use one from the history</option>
+        -->
       </param>
       <when value="indexed">
-        <param name="ref_fastas" type="select" label="Select a reference genome">
+        <param name="ref_fastas" type="select" label="Select a reference genome fasta">
           <options from_data_table="all_fasta">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No reference fasta files are available" />
           </options>
         </param>
-        <param name="twobit_indices" type="select" label="Select a reference genome">
+        <param name="twobit_indices" type="select" label="Select the reference genome 2bit">
           <options from_data_table="twobit">
             <filter type="sort_by" column="0" />
+            <!--
             <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
+            -->
             <validator type="no_options" message="No indexes are available" />
           </options>
         </param>
-        <param name="bwa_indices" type="select" label="Select a reference genome">
+        <param name="bwa_indices" type="select" label="Select the reference genome bwa indices">
           <options from_data_table="bwa_indexes">
             <filter type="sort_by" column="2" />
+            <!--
             <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
+            -->
             <validator type="no_options" message="No indexes are available" />
           </options>
         </param>
       </when>
+      <!--
       <when value="history">
         <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
         <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" />
         <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
       </when>
+      -->
     </conditional>
     <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
   </inputs>