diff cuffdiff_wrapper.xml @ 7:b5562b9a55c7

Use same bias_correction cached param as devteam cuffdiff

--- a/cuffdiff_wrapper.xml	Mon Nov 18 16:43:15 2013 -0600
+++ b/cuffdiff_wrapper.xml	Mon Oct 13 09:12:47 2014 -0500
@@ -40,7 +40,7 @@
                     $bias_correction.seq_source.ref_file
                 #else:
                     ## Built-in genome.
-                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
+                    ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
             #end if
 
@@ -123,7 +123,14 @@
                     <option value="cached">Locally cached</option>
                     <option value="history">History</option>
                   </param>
-                  <when value="cached"></when>
+                  <when value="cached">
+                    <param name="index" type="select" label="Using reference genome">
+                      <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
+                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+                      </options>
+                    </param>
+                  </when>
                   <when value="history">
                       <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                   </when>