diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index a51330524a3..1b1a4757912 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -195,7 +195,7 @@ class DefaultToolAction( object ):
         else:
             # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
             chrom_info = None
-            if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+            if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
                 # Custom build.
                 custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
                 if 'fasta' in custom_build_dict: