diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 0b4666175ab..31f793825b2 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -151,8 +151,8 @@ class Registry( object ):
         # call init_meta and copy metadata from itself.  The datatype
         # being converted *to* will handle any metadata copying and
         # initialization.
-        data.init_meta( copy_from=data )
         if data.has_data():
+            data.init_meta( copy_from=data )
             data.set_peek()
         return data
 
diff --git a/tools/data_source/biomart_filter.py b/tools/data_source/biomart_filter.py
index dddf416a970..3e17b1f0be4 100644
--- a/tools/data_source/biomart_filter.py
+++ b/tools/data_source/biomart_filter.py
@@ -1,7 +1,6 @@
 # Greg Von Kuster
 import urllib
 from galaxy.datatypes import sniff
-
 from galaxy import datatypes, config
 import tempfile, shutil
 
@@ -18,27 +17,21 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
 
 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
     """Verifies the data after the run"""
-
     URL = param_dict.get( 'URL', None )
     if not URL:
         raise Exception('Datasource has not sent back a URL parameter')
     URL = URL + '&_export=1&GALAXY_URL=0'
     CHUNK_SIZE = 2**20 # 1Mb 
     MAX_SIZE   = CHUNK_SIZE * 100
-    
     try:
-        # damn you stupid sanitizer! - URL is now in the NEVER_SANITIZE list in util.py
-        #URL = URL.replace('martX', 'mart&')
-        #URL = URL.replace('0X_', '0&_')
         page = urllib.urlopen(URL)
     except Exception, exc:
         raise Exception('Problems connecting to %s (%s)' % (URL, exc) )
-
     name, data = out_data.items()[0]
-    
     fp = open(data.file_name, 'wb')
     size = 0
     max_size_exceeded = False
+
     while 1:
         chunk = page.read(CHUNK_SIZE)
         if not chunk:
@@ -48,15 +41,15 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
             max_size_exceeded = True
             break
         fp.write(chunk)
-
     fp.close()
     
     if max_size_exceeded:
         data.info = 'Maximum data size of 100 MB exceeded, incomplete data retrieval.'
     else:
         data.info = data.name
-    #Set meta data, format file to be valid interval type
-    if isinstance(data.datatype, datatypes.interval.Interval):
+
+    if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval):
+        #Set meta data, format file to be valid interval type
         data.set_meta(first_line_is_header=True)
         #check for missing meta data, if all there, comment first line and process file
         if not data.missing_meta():
@@ -69,17 +62,13 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
             startCol = int(data.metadata.startCol) - 1
             strandCol = int(data.metadata.strandCol) - 1
             
-            
             for line in open(data.file_name, 'r'):
                 line_ctr += 1
-                
                 #First line is a non-commented header line, lets comment it out here
                 if line_ctr == 0:
                     temp.write("#%s" % line)
                     continue
-                
                 fields = line.strip().split('\t')
-                
                 #If chrom col is an int, make it chrInt
                 try:
                     int(fields[chromCol])
@@ -89,14 +78,12 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
                         if fields[chromCol].upper()== "X" or fields[chromCol].upper()== "Y":
                             fields[chromCol] = "chr%s" % fields[chromCol].upper()
                     except:
-                        pass
-                    
+                        pass 
                 #change to BED coordinate system
                 try:
                     fields[startCol] = str(int(fields[startCol]) - 1)
                 except:
                     pass
-                
                 #set strand to +/-, instead of +1/-1
                 try:
                     if strandCol > 0:
@@ -106,17 +93,18 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
                             fields[strandCol] = "-"
                 except:
                     pass
-                
                 temp.write("%s\n" % '\t'.join(fields))
-            
             temp.close()
             shutil.move(temp_filename,data.file_name)
-            
         else:
             data_type = sniff.guess_ext(data.file_name)
             data = app.datatypes_registry.change_datatype(data, data_type)
+            if data.missing_meta():
+                data.set_meta()
     else:
         data_type = sniff.guess_ext(data.file_name)
         data = app.datatypes_registry.change_datatype(data, data_type)
+        if data.missing_meta():
+            data.set_meta()
     data.set_peek()
     data.flush()