diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index 2618aeaf78b..762e267730d 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -391,6 +391,23 @@
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 ) 
             </filter>
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
         </data>
         <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
             <filter>
@@ -401,9 +418,62 @@
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 )
             </filter>
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
+        </data>
+        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
+        </data>
+        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
+            <actions>
+              <conditional name="refGenomeSource.genomeSource">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                    </option>
+                  </action>
+                </when>
+                <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+                  </action>
+                </when>
+              </conditional>
+            </actions>
         </data>
-        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/>
-        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/>
     </outputs>
     <tests>
         <!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters -->
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index ebd1094c15e..dde33413a22 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -386,7 +386,7 @@
                       ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or 
                     ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and 
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
-                ) 
+                )
             </filter>
             <actions>
               <conditional name="refGenomeSource.genomeSource">