diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 35ee159d60e..73f8431a9cd 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1646,6 +1646,12 @@ class DataSourceTool( Tool ):
             data.name = param_dict.get( 'name', data.name )
             data.info = param_dict.get( 'info', data.name )
             data.dbkey = param_dict.get( 'dbkey', data.dbkey )
+            # HACK to map modENCODEfly dbkey, which is always "fly" to be dm2
+            # and modENCODEworm dbkey, which is always "worm" to be ce6
+            if data.dbkey == 'fly':
+                data.dbkey = 'dm2'
+            elif data.dbkey == 'worm':
+                data.dbkey = 'ce6'
             data.extension = param_dict.get( 'data_type', data.extension )
         #TODO: these should be possible as part of data_source.py and external set_meta, see the upload tool:
         if data.extension in [ 'txt', 'tabular' ]:
diff --git a/tools/data_source/fly_modencode.xml b/tools/data_source/fly_modencode.xml
index e377e0d7e0e..d96d1f2c55d 100644
--- a/tools/data_source/fly_modencode.xml
+++ b/tools/data_source/fly_modencode.xml
@@ -10,7 +10,7 @@
         <request_param galaxy_name="URL" remote_name="URL" missing="">
             <append_param separator="&amp;" first_separator="?" join="=">
                 <value name="d" missing="" />
-                <value name="dbkey" missing="" />
+                <value name="dbkey" missing="dm2" />
                 <value name="q" missing="" />
                 <value name="s" missing="" />
                 <value name="t" missing="" />
diff --git a/tools/data_source/worm_modencode.xml b/tools/data_source/worm_modencode.xml
index 4087a789dfc..cfa02be5a53 100644
--- a/tools/data_source/worm_modencode.xml
+++ b/tools/data_source/worm_modencode.xml
@@ -10,7 +10,7 @@
         <request_param galaxy_name="URL" remote_name="URL" missing="">
             <append_param separator="&amp;" first_separator="?" join="=">
                 <value name="d" missing="" />
-                <value name="dbkey" missing="" />
+                <value name="dbkey" missing="ce6" />
                 <value name="q" missing="" />
                 <value name="s" missing="" />
                 <value name="t" missing="" />