diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 2e2d932a54b..c5bb968cfcf 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -769,16 +769,6 @@ class Tool:
                         errors[ input.name ] = old_errors[ input.name ]
                 else:
                     incoming_value = incoming.get( key, None )
-                    if ( incoming_value == 'None' or incoming_value == '?' ) and ( isinstance( input, SelectToolParameter ) or isinstance( input, DataToolParameter ) ) and input.is_dynamic:
-                        # FIXME: This is a HACK, but is necessary because the
-                        # values in incoming are not yet set by the user when
-                        # the select list is dynamically generated.
-                        legal_values = input.get_legal_values( trans, context )
-                        if len( legal_values ) > 0 and incoming_value not in legal_values:
-                            values = []
-                            for v in legal_values: values.append( v )
-                            values.sort()
-                            incoming_value = values[0]
                     value, error = self.check_param( trans, input, incoming_value, context )
                     if error:
                         errors[ input.name ] = error
diff --git a/lib/galaxy/tools/dynamic_options.py b/lib/galaxy/tools/dynamic_options.py
index e25d105626e..a45b4d9c4ed 100644
--- a/lib/galaxy/tools/dynamic_options.py
+++ b/lib/galaxy/tools/dynamic_options.py
@@ -8,7 +8,11 @@ class DynamicOptions( object ):
     """Handles dynamically generated SelectToolParameter options"""
     def __init__( self, elem, parameter_type = None  ):
         self.parameter_type = parameter_type
+        self.data_ref = None
+        self.param_ref = None
         self.from_file_data = None
+
+        # Parse the options tag
         self.from_file = elem.get( 'from_file', None )
         if self.from_file is not None:
             self.from_file = self.from_file.strip()
@@ -19,17 +23,26 @@ class DynamicOptions( object ):
                 self.data_file = self.from_file
         else: 
             self.data_file = None
+        self.name_col = elem.get( 'name_col', None )
+        if self.name_col is not None:
+            self.name_col = int( self.name_col.strip() )
+        self.value_col = elem.get( 'value_col', None )
+        if self.value_col is not None:
+            self.value_col = int( self.value_col.strip() )
+        
+        # Parse the filter tags
         self.filters = elem.findall( 'filter' )
-        self.data_ref = None
-        self.param_ref = None
         for filter in self.filters:
             filter_type = filter.get( 'type', None )
             assert filter_type is not None, "Required 'type' attribute missing from filter"
-            if filter_type.strip() == 'data_meta':
+            filter_type = filter_type.strip()
+
+            if filter_type == 'data_meta':
                 self.data_ref = filter.get( 'data_ref', None )
                 assert self.data_ref is not None, "Required 'data_ref' attribute missing from 'data_meta' filter"
                 self.data_ref = self.data_ref.strip()
-            elif filter_type.strip() == 'param_meta':
+
+            elif filter_type == 'param_meta':
                 self.param_ref = filter.get( 'param_ref', None )
                 assert self.param_ref is not None, "Required 'param_ref' attribute missing from 'param_meta' filter"
                 self.param_ref = self.param_ref.strip()
@@ -74,31 +87,38 @@ class DynamicOptions( object ):
         # Check for filters and build a dictionary from them
         for filter in self.filters:
             filter_type = filter.get( 'type', None )
-            assert filter_type is not None, "type attribute missing from filter"
+            assert filter_type is not None, "'type' attribute missing from filter"
             filter_type = filter_type.strip()
+
             if filter_type == 'data_meta':
                 filters[ 'data_meta' ] = {}
                 dataset = self.get_data_ref_value( trans, other_values )
                 if dataset is None: 
                     return []
-                key = filter.get( 'key', None )
-                if key is not None:
-                    filters[ 'data_meta' ][ 'key' ] = key.strip()
-                value = filter.get( 'value', None )
-                if value is not None: 
-                    value = value.strip()
-                else:
-                    if key == 'build': 
-                        value = dataset.get_dbkey()
-                    elif key == 'file_name': 
-                        value = dataset.get_file_name()
-                    elif key == 'species': 
-                        value = dataset.metadata.species
-                filters[ 'data_meta' ][ 'value' ] = value
+                # meta_key is optional
+                meta_key = filter.get( 'meta_key', None )
+                if meta_key is not None:
+                    filters[ 'data_meta' ][ 'meta_key' ] = meta_key.strip()
+                    if meta_key == 'dbkey':
+                        meta_value = dataset.get_dbkey()
+                    elif meta_key == 'species': 
+                        meta_value = dataset.metadata.species
+                    filters[ 'data_meta' ][ 'meta_value' ] = meta_value
+                elif self.data_file == 'data_ref':
+                    # We'll be reading data directly from the input dataset
+                    filters[ 'data_meta' ][ 'meta_key' ] = 'data_ref'
+                    self.from_file = dataset.get_file_name()
+                    filters[ 'data_meta' ][ 'meta_value' ] = self.from_file
+                # meta_key_col is optional
+                meta_key_col = filter.get( 'meta_key_col', None )
+                if meta_key_col is not None:
+                    filters[ 'data_meta' ][ 'meta_key_col' ] = int( meta_key_col.strip() )
+
             elif filter_type == 'param_meta':
                 filters[ 'param_meta' ] = {}
-                value = self.get_param_ref_value( trans, other_values )
-                filters[ 'param_meta' ][ 'value' ] = value
+                meta_value = self.get_param_ref_value( trans, other_values )
+                filters[ 'param_meta' ][ 'meta_value' ] = meta_value
+
             elif filter_type == 'param_value':
                 n = filter.get( 'name', None )
                 assert n is not None, "param_value filters require a 'name' attribute"
@@ -111,18 +131,7 @@ class DynamicOptions( object ):
                 except:
                     filters[ 'param_values' ] = {}
                     filters[ 'param_values' ][ n ] = v
-            elif filter_type == 'column':
-                n = filter.get( 'name', None )
-                assert n is not None, "column filters require a 'name' attribute"
-                n = n.strip()
-                v = filter.get( 'value', None )
-                assert v is not None, "column filters require a 'value' attribute"
-                v = v.strip()
-                try: 
-                    filters[ 'columns' ][ n ] = v
-                except: 
-                    filters[ 'columns' ] = {}
-                    filters[ 'columns' ][ n ] = v
+
             elif filter_type == 'param':
                 n = filter.get( 'name', None )
                 assert n is not None, "param filters require a 'name' attribute"
@@ -137,50 +146,47 @@ class DynamicOptions( object ):
                     filters[ 'params' ][ n ] = v
         # Now that we've parsed our filters, we need to see if the tool is a maf tool 
         # which requires special handling
+        # TODO: remove or rework this if possible
         try:
             maf_source = filters[ 'params' ][ 'maf_source' ]
             if maf_source == 'cached':
-                maf_uid = filters[ 'param_meta' ][ 'value' ]
+                maf_uid = filters[ 'param_meta' ][ 'meta_value' ]
                 if maf_uid in [ None, 'None' ]:
                     return []
                 return self.generate_for_maf( maf_uid, '\t' )
             elif maf_source == 'user':
                 dataset = self.get_data_ref_value( trans, other_values )
-                filters[ 'data_meta' ][ 'key' ] = 'species'
-                filters[ 'data_meta' ][ 'value' ] = dataset.metadata.species
+                filters[ 'data_meta' ][ 'meta_key' ] = 'species'
+                filters[ 'data_meta' ][ 'meta_value' ] = dataset.metadata.species
         except:
             pass
-        return self.generate_options( filters )
+        return self.generate_options( filters=filters, sep='\t' )
     def generate_options( self, filters={}, sep='\t' ):
         try: 
-            key = filters[ 'data_meta' ][ 'key' ]
+            meta_key = filters[ 'data_meta' ][ 'meta_key' ]
         except:
             try: 
-                key = filters[ 'param_meta' ][ 'key' ]
+                meta_key = filters[ 'param_meta' ][ 'meta_key' ]
             except: 
-                key = None
-        if key == 'species':
-            species = filters[ 'data_meta' ][ 'value' ]
-            return self.generate_for_species( species )
-        elif key == 'file_name':
-            file_name = filters[ 'data_meta' ][ 'value' ]
-            value_col = int( filters[ 'columns' ][ 'value_col' ] )
-            return self.generate_from_dataset( file_name, value_col, sep )
-        elif key == 'build':
-            build = filters[ 'data_meta' ][ 'value' ]
+                meta_key = None
+        if meta_key == 'species':
+            return self.generate_for_species( filters[ 'data_meta' ][ 'meta_value' ] )
+        elif meta_key == 'data_ref':
+            dataset_file_name = filters[ 'data_meta' ][ 'meta_value' ]
+            return self.generate_from_dataset( dataset_file_name, self.value_col, sep )
+        elif meta_key == 'dbkey':
+            dbkey = filters[ 'data_meta' ][ 'meta_value' ]
             if self.parameter_type == parameters.DataToolParameter:
-                return key, build
-            build_col = int( filters[ 'columns' ][ 'build_col' ].strip() )
-            name_col = int( filters[ 'columns' ][ 'name_col' ] )
-            value_col = int( filters[ 'columns' ][ 'value_col' ] )
-            return self.generate_for_build( build, build_col, name_col, value_col, sep )
-        else: # key is None
+                return meta_key, dbkey
+            meta_key_col = filters[ 'data_meta' ][ 'meta_key_col' ]
+            return self.generate_for_build( dbkey, meta_key_col, self.name_col, self.value_col, sep )
+        else: # meta_key is None
             if self.data_file == 'datatypes_registry':
                 return self.generate_from_datatypes_registry()
             elif self.data_file == 'encode_datasets.loc':
                 encode_group = filters[ 'params' ][ 'encode_group' ]
-                build = filters[ 'params' ][ 'build' ]
-                return self.generate_for_encode( encode_group, build, sep )
+                dbkey = filters[ 'params' ][ 'dbkey' ]
+                return self.generate_for_encode( encode_group, dbkey, sep )
             elif self.data_file == 'microbial_data.loc':
                 if self.from_file_data is None: 
                     self.load_microbial_data()
@@ -198,9 +204,7 @@ class DynamicOptions( object ):
                     feature = None
                 return self.generate_for_microbial( kingdom, org, feature )
             else:
-                name_col = int( filters[ 'columns' ][ 'name_col' ] )
-                value_col = int( filters[ 'columns' ][ 'value_col' ] )
-                return self.generate( name_col, value_col, sep )
+                return self.generate( self.name_col, self.value_col, sep )
     def generate_from_datatypes_registry( self ):
         from galaxy.datatypes import registry
         datatypes_registry = registry.Registry()
@@ -212,7 +216,7 @@ class DynamicOptions( object ):
             label = format.capitalize()
             options.append( ( label, format, False ) )
         return options
-    def generate_for_encode( self, encode_group, build, sep ):
+    def generate_for_encode( self, encode_group, dbkey, sep ):
         options = []
         def generate():
             encode_sets = {}
@@ -222,7 +226,7 @@ class DynamicOptions( object ):
                     try:
                         fields = line.split( sep )
                         encode_group = fields[ 0 ]
-                        build = fields[ 1 ]
+                        dbkey = fields[ 1 ]
                         description = fields[ 2 ]
                         uid = fields[ 3 ]
                         path = fields[ 4 ]
@@ -242,15 +246,15 @@ class DynamicOptions( object ):
                     except: 
                         encode_sets[ encode_group ] = {}
                     try:
-                        encode_sets[ encode_group ][ build ].append( ( description, uid, False ) )
+                        encode_sets[ encode_group ][ dbkey ].append( ( description, uid, False ) )
                     except:
-                        encode_sets[ encode_group ][ build ] = []
-                        encode_sets[ encode_group ][ build] .append( ( description, uid, False ) )
+                        encode_sets[ encode_group ][ dbkey ] = []
+                        encode_sets[ encode_group ][ dbkey].append( ( description, uid, False ) )
             #Order by description and date, highest date on top and bold
             for group in encode_sets:
-                for build in encode_sets[ group ]:
-                    ordered_build = []
-                    for description, uid, selected in encode_sets[ group ][ build ]:
+                for dbkey in encode_sets[ group ]:
+                    ordered_dbkey = []
+                    for description, uid, selected in encode_sets[ group ][ dbkey ]:
                         item = {}
                         item[ 'date' ] = 0
                         item[ 'description' ] = ""
@@ -265,32 +269,32 @@ class DynamicOptions( object ):
                             item[ 'date' ] = description[ -9:-1 ]
                             item[ 'description' ] = description[ 0:-10 ]
                             
-                        for i in range( len( ordered_build ) ):
-                            ordered_description, ordered_uid, ordered_selected, ordered_item = ordered_build[ i ]
+                        for i in range( len( ordered_dbkey ) ):
+                            ordered_description, ordered_uid, ordered_selected, ordered_item = ordered_dbkey[ i ]
                             if item[ 'description' ] < ordered_item[ 'description' ]:
-                                ordered_build.insert( i, ( description, uid, selected, item ) )
+                                ordered_dbkey.insert( i, ( description, uid, selected, item ) )
                                 break
                             if item[ 'description' ] == ordered_item[ 'description' ] and item[ 'partitioned' ] == ordered_item[ 'partitioned' ]:
                                 if int( item[ 'date' ] ) > int( ordered_item[ 'date' ] ):
-                                    ordered_build.insert( i, ( description, uid, selected, item ) )
+                                    ordered_dbkey.insert( i, ( description, uid, selected, item ) )
                                     break
                         else: 
-                            ordered_build.append( ( description, uid, selected, item ) )
+                            ordered_dbkey.append( ( description, uid, selected, item ) )
                     last_desc = None
                     last_partitioned = None
-                    for i in range( len( ordered_build ) ) :
-                        description, uid, selected, item = ordered_build[ i ]
+                    for i in range( len( ordered_dbkey ) ) :
+                        description, uid, selected, item = ordered_dbkey[ i ]
                         if item[ 'partitioned' ] != last_partitioned or last_desc != item[ 'description' ]:
                             last_desc = item[ 'description' ]
                             description = "<b>" + description + "</b>"
                         else:
                             last_desc = item[ 'description' ]
                         last_partitioned = item[ 'partitioned' ]
-                        encode_sets[ group ][ build ][ i ] = ( description, uid, selected )        
+                        encode_sets[ group ][ dbkey ][ i ] = ( description, uid, selected )        
             return encode_sets
         d = generate()
         try: 
-            options = d[ encode_group ][ build ][ 0: ]
+            options = d[ encode_group ][ dbkey ][ 0: ]
         except:
             return []
         return options
@@ -464,14 +468,6 @@ class DynamicOptions( object ):
             line = line.rstrip( '\r\n' )
             if line and not line.startswith( '#' ):
                 fields = line.split( sep )
-                # TDDO: regenerate the following data files so that they follow a column standard.
-                # build_col = 0 - put build values in column 0
-                # name_col = 1 - put the select list description values in column 1
-                # value_col = 2 - put the select list value values in column 2
-                # This will allow us to eliminate the following data_file conditionals
-                #
-                # TODO: the alignseq.loc file is currently ony used by the "Extract blastz alignments1"
-                # tool, which seems to be deprecated.  Can we eliminate it altogether?
                 if self.data_file == 'alignseq.loc':
                     if fields[ build_col ].strip() == 'align':
                         try: 
@@ -497,9 +493,6 @@ class DynamicOptions( object ):
                         d[ maf_uid ][ 'builds' ] = build_list
                     except: 
                         continue
-
-        # TODO: the alignseq.loc file is currently ony used by the "Extract blastz alignments1"
-        # tool, which seems to be deprecated.  Can we eliminate it altogether?
         if self.data_file == 'alignseq.loc':
             # FIXME: We need a database of descriptive names corresponding to dbkeys.
             #        We need to resolve the musMusX <--> mmX confusion
diff --git a/tools/data_source/encode_import_all_latest_datasets.xml b/tools/data_source/encode_import_all_latest_datasets.xml
index f07173f9c00..7d5042a5b46 100644
--- a/tools/data_source/encode_import_all_latest_datasets.xml
+++ b/tools/data_source/encode_import_all_latest_datasets.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="ALD" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="ALD" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/data_source/encode_import_chromatin_and_chromosomes.xml b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
index bf0dd376d98..643fe335937 100644
--- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml
+++ b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="CC" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="CC" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/data_source/encode_import_gencode.xml b/tools/data_source/encode_import_gencode.xml
index 2767c4b654c..2be284c36ed 100644
--- a/tools/data_source/encode_import_gencode.xml
+++ b/tools/data_source/encode_import_gencode.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="GENCODE" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="GENCODE" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/data_source/encode_import_genes_and_transcripts.xml b/tools/data_source/encode_import_genes_and_transcripts.xml
index de1ce839c7e..489a8c952d2 100644
--- a/tools/data_source/encode_import_genes_and_transcripts.xml
+++ b/tools/data_source/encode_import_genes_and_transcripts.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="GT" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="GT" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/data_source/encode_import_multi-species_sequence_analysis.xml b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
index c89122be885..7b518eb544b 100644
--- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml
+++ b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="MSA" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="MSA" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/data_source/encode_import_transcription_regulation.xml b/tools/data_source/encode_import_transcription_regulation.xml
index 29efe16da3c..bfea84c1e81 100644
--- a/tools/data_source/encode_import_transcription_regulation.xml
+++ b/tools/data_source/encode_import_transcription_regulation.xml
@@ -8,13 +8,13 @@
     <param name="hg17" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="TR" />
-        <filter type="param" name="build" value="hg17" />
+        <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
       <options from_file="/depot/data2/galaxy/encode_datasets.loc">
         <filter type="param" name="encode_group" value="TR" />
-        <filter type="param" name="build" value="hg16" />
+        <filter type="param" name="dbkey" value="hg16" />
       </options>
     </param> 
   </inputs>
diff --git a/tools/encode/random_intervals1/1.0.0/random_intervals.xml b/tools/encode/random_intervals1/1.0.0/random_intervals.xml
index 3278de9d3bd..b919c414a04 100644
--- a/tools/encode/random_intervals1/1.0.0/random_intervals.xml
+++ b/tools/encode/random_intervals1/1.0.0/random_intervals.xml
@@ -16,20 +16,10 @@
       <option value="none">None</option>
     </param>
     <param name="regions" type="select" label="Regions to use">
-      <options from_file="/depot/data2/galaxy/regions.loc" >
-        <filter type="data_meta" data_ref="input1" key="build" />
-        <filter type="column" name="build_col" value="0" />
-        <filter type="column" name="name_col" value="2" />
-        <filter type="column" name="value_col" value="1" />
+      <options from_file="/depot/data2/galaxy/regions.loc" name_col="2" value_col="1">
+        <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="0" />
       </options>
     </param> 
-    <!--
-    <param name="regions" type="select" label="Regions to use">
-      <options from_file="/depot/data2/galaxy/phastOdds.loc" name_col="2" value_col="1">
-        <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0" />
-      </options>
-    </param> 
-    -->
   </inputs>
   <outputs>
     <data name="out_file1" format="input"/>
diff --git a/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml b/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml
index a623d951659..d800ca72245 100644
--- a/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml
+++ b/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml
@@ -2,16 +2,13 @@
   <description>between query genome and another genome</description>
   <command interpreter="perl">extractAxt_wrapper.pl -i $input -o $out_file1 --species $species -g $dbkey $input_chromCol $input_startCol $input_endCol $input_strandCol</command>
   <inputs>
-    <param format="interval" name="input" type="data" label="Between regions of Query"/>
+    <param format="interval" name="input" type="data" label="Between regions of Query"/>    
     <param name="species" type="select" label="and one of these genomes">
       <validator type="unspecified_build" />
-      <options from_file="/depot/data2/galaxy/alignseq.loc" >
-        <filter type="data_meta" data_ref="input" key="build" />
-        <filter type="column" name="build_col" value="0" />
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="2" />
+      <options from_file="/depot/data2/galaxy/alignseq.loc" name_col="1" value_col="2">
+        <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0" />
       </options>
-    </param> 
+    </param>    
   </inputs>
   <outputs>
     <data format="axt" name="out_file1" />
diff --git a/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml b/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml
index c7f7f3ef5a2..2762ac9da2d 100644
--- a/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml
+++ b/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml
@@ -13,51 +13,40 @@
       </param>
       <when value="0">
         <param name="feature" type="select" multiple="true" label="Select features" >
-          <options>
-            <filter type="data_meta" data_ref="input1" key="file_name" />
-            <filter type="column" name="value_col" value="0" />
+          <options from_file="data_ref" value_col="0">
+            <filter type="data_meta" data_ref="input1" />
           </options>
         </param> 
       </when>
       <when value="1">
         <param name="feature" type="select" multiple="true" label="Select features" >
-          <options>
-            <filter type="data_meta" data_ref="input1" key="file_name" />
-            <filter type="column" name="value_col" value="1" />
+          <options from_file="data_ref" value_col="1">
+            <filter type="data_meta" data_ref="input1" />
           </options>
-        </param>         	
+        </param>        	
       </when>
       <when value="2">
         <param name="feature" type="select" multiple="true" label="Select features" >
-          <options>
-            <filter type="data_meta" data_ref="input1" key="file_name" />
-            <filter type="column" name="value_col" value="2" />
+          <options from_file="data_ref" value_col="2">
+            <filter type="data_meta" data_ref="input1" />
           </options>
-        </param>          	
+        </param> 
       </when>
       <when value="6">
         <param name="feature" type="select" multiple="true" label="Select features" >
-          <options>
-            <filter type="data_meta" data_ref="input1" key="file_name" />
-            <filter type="column" name="value_col" value="6" />
+          <options from_file="data_ref" value_col="6">
+            <filter type="data_meta" data_ref="input1" />
           </options>
-        </param>           	
+        </param>         	
       </when>
       <when value="7">
         <param name="feature" type="select" multiple="true" label="Select features" >
-          <options>
-            <filter type="data_meta" data_ref="input1" key="file_name" />
-            <filter type="column" name="value_col" value="7" />
+          <options from_file="data_ref" value_col="7">
+            <filter type="data_meta" data_ref="input1" />
           </options>
-        </param>              	
+        </param>            	
       </when>
     </conditional>
-    <!--
-    <param name="out_format" type="select" label="Output format">
-      <option value="GFF" selected="true">GFF</option>
-      <option value="BED">BED</option>
-    </param>
-    -->
   </inputs>
   <outputs>
     <data format="gff" name="out_file1" />
diff --git a/tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml b/tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml
index 5699397b02a..47e085efbe0 100644
--- a/tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml
+++ b/tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml
@@ -6,13 +6,10 @@
       <validator type="unspecified_build" />
     </param>
     <param name="to_dbkey" type="select" label="To">
-      <options from_file="/depot/data2/galaxy/liftOver.loc">
-        <filter type="data_meta" data_ref="input" key="build" />
-        <filter type="column" name="build_col" value="0" />
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="1" />
+      <options from_file="/depot/data2/galaxy/liftOver.loc" name_col="1" value_col="1">
+        <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0"/>
       </options>
-    </param>
+    </param> 
   </inputs>
   <outputs>
     <data format="bed" name="out_file1" />
diff --git a/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml
index 2032189fdec..d0636ae4c13 100644
--- a/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml
@@ -6,11 +6,8 @@
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
     </param>
     <param name="score_file" type="select" label="Available datasets">
-      <options from_file="/depot/data2/galaxy/phastOdds.loc" >
-        <filter type="data_meta" data_ref="input" key="build" />
-        <filter type="column" name="build_col" value="0" />
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="2" />
+      <options from_file="/depot/data2/galaxy/phastOdds.loc" name_col="1" value_col="2">
+        <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0"/>
       </options>
     </param> 
 	<param name="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
diff --git a/tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml b/tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml
index 96144009be4..cb9db77a911 100644
--- a/tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml
+++ b/tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml
@@ -4,16 +4,10 @@
   <inputs>
     <param format="axt" name="axt_input" type="data" label="AXT file"/>
     <param name="dbkey_1" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
     <param name="dbkey_2" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
   </inputs>
   <outputs>
diff --git a/tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.xml b/tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.xml
index 67cdc3465e0..0370cc692c6 100644
--- a/tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.xml
+++ b/tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.xml
@@ -4,16 +4,10 @@
   <inputs>
     <param format="axt" name="axt_input" type="data" label="AXT file"/>
     <param name="dbkey_1" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
     <param name="dbkey_2" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
   </inputs>
   <outputs>
diff --git a/tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.xml b/tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.xml
index b46794e6226..747cca001f4 100644
--- a/tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.xml
+++ b/tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.xml
@@ -5,16 +5,10 @@
   <inputs>
     <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/>
     <param name="dbkey_1" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
     <param name="dbkey_2" type="select" label="Genome">
-      <options from_file="static/ucsc/builds.txt" >
-        <filter type="column" name="name_col" value="1" />
-        <filter type="column" name="value_col" value="0" />
-      </options>
+      <options from_file="static/ucsc/builds.txt" name_col="1" value_col="0" />
     </param> 
   </inputs>
   <outputs>
diff --git a/tools/maf/GeneBed_Maf_Fasta2/1.0.0/genebed_maf_to_fasta.xml b/tools/maf/GeneBed_Maf_Fasta2/1.0.0/genebed_maf_to_fasta.xml
index 4a7fc5bb7d6..532f655a3fb 100644
--- a/tools/maf/GeneBed_Maf_Fasta2/1.0.0/genebed_maf_to_fasta.xml
+++ b/tools/maf/GeneBed_Maf_Fasta2/1.0.0/genebed_maf_to_fasta.xml
@@ -26,11 +26,8 @@
       </when>
       <when value="cached">
         <param name="maf_identifier" type="select" label="MAF Type" >
-          <options from_file="/depot/data2/galaxy/maf_index.loc" >
-            <filter type="data_meta" data_ref="input1" key="build" />
-            <filter type="column" name="build_col" value="2" />
-            <filter type="column" name="name_col" value="0" />
-            <filter type="column" name="value_col" value="1" />
+          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+            <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
         </param> 
         <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
diff --git a/tools/maf/Interval2Maf1/1.0.0/interval2maf.xml b/tools/maf/Interval2Maf1/1.0.0/interval2maf.xml
index 72662e77281..8eb178515b2 100644
--- a/tools/maf/Interval2Maf1/1.0.0/interval2maf.xml
+++ b/tools/maf/Interval2Maf1/1.0.0/interval2maf.xml
@@ -21,11 +21,8 @@
       </when>
       <when value="cached">
         <param name="mafType" type="select" label="Choose alignments">
-          <options from_file="/depot/data2/galaxy/maf_index.loc" >
-            <filter type="data_meta" data_ref="input1" key="build" />
-            <filter type="column" name="build_col" value="2" />
-            <filter type="column" name="name_col" value="0" />
-            <filter type="column" name="value_col" value="1" />
+          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+            <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
         </param> 
       </when>
diff --git a/tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf_pairwise.xml b/tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf_pairwise.xml
index 684d832d5b5..29e3a0cbb2f 100644
--- a/tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf_pairwise.xml
+++ b/tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf_pairwise.xml
@@ -6,13 +6,10 @@
       <validator type="unspecified_build" />
     </param>
     <param name="mafType" type="select" label="Choose MAF source">
-      <options from_file="/depot/data2/galaxy/maf_pairwise.loc">
-        <filter type="data_meta" data_ref="input1" key="build" />
-        <filter type="column" name="build_col" value="2" />
-        <filter type="column" name="name_col" value="0" />
-        <filter type="column" name="value_col" value="1" />
+      <options from_file="/depot/data2/galaxy/maf_pairwise.loc" name_col="0" value_col="1">
+        <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
       </options>
-    </param>
+    </param> 
    </inputs>
   <outputs>
     <data format="maf" name="out_file1" />
diff --git a/tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.xml b/tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.xml
index 6463b1e0f8d..d5f14672404 100644
--- a/tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.xml
+++ b/tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.xml
@@ -26,12 +26,9 @@
               </param>
             </when>
             <when value="cached">
-              <param name="maf_identifier" type="select" label="MAF Type">
-                <options from_file="/depot/data2/galaxy/maf_index.loc">
-                  <filter type="data_meta" data_ref="input1" key="build" />
-                  <filter type="column" name="build_col" value="2" />
-                  <filter type="column" name="name_col" value="0" />
-                  <filter type="column" name="value_col" value="1" />
+              <param name="maf_identifier" type="select" label="MAF Type" >
+                <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+                  <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
                 </options>
               </param> 
               <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
diff --git a/tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml b/tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml
index 8baf143d170..2ea6d6a0f01 100644
--- a/tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml
+++ b/tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml
@@ -13,7 +13,7 @@
     </param>
     <param name="species" type="select" label="Species to keep" display="checkboxes" multiple="true">
       <options>
-        <filter type="data_meta" data_ref="input1" key="species" />
+        <filter type="data_meta" data_ref="input1" meta_key="species" />
       </options>
     </param>
   </inputs>
diff --git a/tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml b/tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml
index 3b39038156c..fbd41448cfc 100644
--- a/tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml
+++ b/tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml
@@ -5,7 +5,7 @@
     <param format="maf" name="input1" type="data" label="MAF file"/>
     <param name="species" type="select" label="Species to keep" display="checkboxes" multiple="true">
       <options>
-        <filter type="data_meta" data_ref="input1" key="species" />
+        <filter type="data_meta" data_ref="input1" meta_key="species" />
       </options>
     </param>
   </inputs>
diff --git a/tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.xml b/tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.xml
index eb37d597f46..cc2b4cf7bb6 100644
--- a/tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.xml
+++ b/tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.xml
@@ -5,7 +5,7 @@
     <param format="maf" name="input1" type="data" label="MAF file to convert"/>
     <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species">
       <options>
-        <filter type="data_meta" data_ref="input1" key="species" />
+        <filter type="data_meta" data_ref="input1" meta_key="species" />
       </options>
     </param>
     <param name="complete_blocks" type="select" label="Exclude blocks which have a requested species missing">
diff --git a/tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta.xml b/tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta.xml
index 564b2a559bc..8ce5ef2db52 100644
--- a/tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta.xml
+++ b/tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta.xml
@@ -15,7 +15,7 @@
       <when value="multiple">
         <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="checked taxa will be included in the output">
           <options>
-            <filter type="data_meta" data_ref="input1" key="species" />
+            <filter type="data_meta" data_ref="input1" meta_key="species" />
           </options>
         </param>
 	    <param name="complete_blocks" type="select" label="Choose to">
@@ -26,7 +26,7 @@
       <when value="concatenated">
         <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true">
           <options>
-            <filter type="data_meta" data_ref="input1" key="species" />
+            <filter type="data_meta" data_ref="input1" meta_key="species" />
           </options>
         </param>
       </when>
diff --git a/tools/maf/MAF_filter/1.0.0/maf_filter.xml b/tools/maf/MAF_filter/1.0.0/maf_filter.xml
index 4c88ebd0949..132134e5a5d 100644
--- a/tools/maf/MAF_filter/1.0.0/maf_filter.xml
+++ b/tools/maf/MAF_filter/1.0.0/maf_filter.xml
@@ -7,7 +7,7 @@
       <repeat name="maf_filters" title="Filter">
         <param name="species1" type="select" label="When Species" multiple="false">
           <options>
-            <filter type="data_meta" data_ref="input1" key="species" />
+            <filter type="data_meta" data_ref="input1" meta_key="species" />
           </options>
         </param>
         <conditional name="species1_attributes">
@@ -27,7 +27,7 @@
             <repeat name="filter_condition" title="Filter Condition">
               <param name="species2" type="select" label="Species" multiple="false">
                 <options>
-                  <filter type="data_meta" data_ref="input1" key="species" />
+                  <filter type="data_meta" data_ref="input1" meta_key="species" />
                 </options>
               </param>
               <conditional name="species2_attributes">
@@ -64,7 +64,7 @@
             <repeat name="filter_condition" title="Filter Condition">
               <param name="species2" type="select" label="Species" multiple="false">
                 <options>
-                  <filter type="data_meta" data_ref="input1" key="species" />
+                  <filter type="data_meta" data_ref="input1" meta_key="species" />
                 </options>
               </param>
               <conditional name="species2_attributes">
diff --git a/tools/maf/maf_stats1/1.0.0/maf_stats.xml b/tools/maf/maf_stats1/1.0.0/maf_stats.xml
index 993cc8ca1f7..19574aab2d5 100644
--- a/tools/maf/maf_stats1/1.0.0/maf_stats.xml
+++ b/tools/maf/maf_stats1/1.0.0/maf_stats.xml
@@ -24,11 +24,8 @@
       </when>
       <when value="cached">
         <param name="mafType" type="select" label="MAF Type">
-          <options from_file="/depot/data2/galaxy/maf_index.loc" >
-            <filter type="data_meta" data_ref="input1" key="build" />
-            <filter type="column" name="build_col" value="2" />
-            <filter type="column" name="name_col" value="0" />
-            <filter type="column" name="value_col" value="1" />
+          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+            <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
         </param> 
       </when>
diff --git a/tools/regVariation/getIndels_3way/1.0.0/getIndels_3way.xml b/tools/regVariation/getIndels_3way/1.0.0/getIndels_3way.xml
index 0be32f5f31d..54261b5c19a 100644
--- a/tools/regVariation/getIndels_3way/1.0.0/getIndels_3way.xml
+++ b/tools/regVariation/getIndels_3way/1.0.0/getIndels_3way.xml
@@ -8,7 +8,7 @@
     	<param format="maf" name="input1" type="data" label="Select data"/>
     	<param name="outgroup" type="select" label="Select outgroup species">
           <options>
-            <filter type="data_meta" data_ref="input1" key="species" />
+            <filter type="data_meta" data_ref="input1" meta_key="species" />
           </options>  
       	</param>
     </page>
diff --git a/tools/regVariation/qualityFilter/1.0.0/quality_filter.xml b/tools/regVariation/qualityFilter/1.0.0/quality_filter.xml
index cb7566ae435..45b0d1b0e67 100644
--- a/tools/regVariation/qualityFilter/1.0.0/quality_filter.xml
+++ b/tools/regVariation/qualityFilter/1.0.0/quality_filter.xml
@@ -20,12 +20,12 @@
     <param format="maf" name="input" type="data" label="Select data"/>
     <param name="primary_species" type="select" label="Use quality scores of" display="checkboxes" multiple="true">
       <options>
-        <filter type="data_meta" data_ref="input" key="species" />
+        <filter type="data_meta" data_ref="input" meta_key="species" />
       </options>  
     </param>
 	<param name="mask_species" type="select" label="Mask Species" display="checkboxes" multiple="true">
       <options>
-        <filter type="data_meta" data_ref="input" key="species" />
+        <filter type="data_meta" data_ref="input" meta_key="species" />
       </options>  
 	</param>
 	<param name="score" size="10" type="integer" value="20" label="Quality score cut-off" help="Cut-off value of 20 means mask all nucleotides having quality score less than or equal to 20"/>
diff --git a/tools/stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml
index 3f9c95f464f..3bab4584b09 100644
--- a/tools/stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml
@@ -16,18 +16,15 @@
       </param>
       <when value="cached">
         <param name="datasets" type="select" label="Available datasets" display="radio">
-          <options from_file="/depot/data2/galaxy/binned_scores.loc" >
-            <filter type="data_meta" data_ref="input1" key="build" />
-            <filter type="column" name="build_col" value="0" />
-            <filter type="column" name="name_col" value="1" />
-            <filter type="column" name="value_col" value="2" />
+          <options from_file="/depot/data2/galaxy/binned_scores.loc" name_col="1" value_col="2">
+            <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="0"/>
           </options>
-       </param>
+        </param>
       </when>
       <when value="user">
         <param format="wig" name="input2" type="data" label="Score file">
           <options>
-            <filter type="data_meta" data_ref="input1" key="build" />
+            <filter type="data_meta" data_ref="input1" meta_key="dbkey" />
           </options>
         </param>
       </when>