diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index e4902521a3a..7db33f2e7d7 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -150,7 +150,6 @@
     <sniffer order="05" type="galaxy.datatypes.sequence:Maf"/>
     <sniffer order="10" type="galaxy.datatypes.sequence:Lav"/>
     <sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/>
-    <sniffer order="20" type="galaxy.datatypes.sequence:Fastq"/>
     <sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/>
     <sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/>
     <sniffer order="35" type="galaxy.datatypes.images:Html"/>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 30cb7b8568b..4abc868e9fe 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -23,6 +23,7 @@ from galaxy.tools.test import ToolTestBuilder
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.model import directory_hash_id
 from galaxy.util.none_like import NoneDataset
+from galaxy.datatypes import sniff
 
 log = logging.getLogger( __name__ )
 
@@ -1140,22 +1141,21 @@ class Tool:
                 description = param_dict.get( 'position', '' )
                 if not description:
                     description = 'unknown position'
-            data_type = param_dict.get( 'data_type ')
+            data_type = param_dict.get( 'data_type' )
             items = out_data.items()
             for name, data in items:
                 if organism and table and description:
                     data.name  = '%s on %s: %s (%s)' % ( data.name, organism, table, description )
                 data.info = info
                 data.dbkey = dbkey
-                ext = data_type
-                try: 
-                    ext = data_type_to_ext[ data_type ]
+                try:
+                    data_type = data_type_to_ext[ data_type ]
                 except: 
                     pass
-                if ext not in app.datatypes_registry.datatypes_by_extension: 
-                    ext = 'interval'
-                data = app.datatypes_registry.change_datatype( data, ext )
-                # store external data source's request parameters temporarily in output file
+                if data_type not in app.datatypes_registry.datatypes_by_extension: 
+                    data_type = 'interval'
+                data = app.datatypes_registry.change_datatype( data, data_type )
+                # Store external data source's request parameters temporarily in output file
                 out = open( data.file_name, 'w' )
                 for key, value in param_dict.items():
                     print >> out, '%s\t%s' % ( key, value )
@@ -1168,9 +1168,15 @@ class Tool:
         # tag set in the tool config.
         if self.tool_type == 'data_source':
             name, data = out_data.items()[0]
-            if data.state == data.states.OK and not data.info:
-                data.info = data.name
-            if not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ):
+            if data.state == data.states.OK:
+                data.name = param_dict.get( 'name', data.name )
+                data.info = param_dict.get( 'info', data.name )
+                data.dbkey = param_dict.get( 'dbkey', data.dbkey )
+                data.extension = param_dict.get( 'data_type', data.extension )
+            if data.extension == 'txt':
+                data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order )
+                data = app.datatypes_registry.change_datatype( data, data_type )
+            elif not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ):
                 data.set_meta()
                 if data.missing_meta(): 
                     data = app.datatypes_registry.change_datatype( data, 'tabular' )
diff --git a/lib/galaxy/util/none_like.py b/lib/galaxy/util/none_like.py
index 1d5295082bd..67b8f3ea0f1 100644
--- a/lib/galaxy/util/none_like.py
+++ b/lib/galaxy/util/none_like.py
@@ -23,7 +23,7 @@ class NoneDataset( RecursiveNone ):
         if datatypes_registry is None: datatypes_registry = Registry()
         self.datatype = datatypes_registry.get_datatype_by_extension( ext )
         self._metadata = None
-        self.metadata = MetadataCollection( self, self.datatype.metadata_spec )
+        self.metadata = MetadataCollection( self )
     def __getattr__( self, name ):
         return "None"
     def missing_meta( self ):
diff --git a/tools/data_source/flymine.xml b/tools/data_source/flymine.xml
index b8e0b9ad2d7..73b1727453d 100644
--- a/tools/data_source/flymine.xml
+++ b/tools/data_source/flymine.xml
@@ -14,7 +14,7 @@
         <request_param galaxy_name="description" remote_name="description" missing="" />
         <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
         <request_param galaxy_name="info" remote_name="info" missing="" />
-        <request_param galaxy_name="data_type" remote_name="data_type" missing="interval" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
     </request_param_translation>
     <uihints minwidth="800"/>
     <outputs>
diff --git a/tools/data_source/ucsc_tablebrowser.xml b/tools/data_source/ucsc_tablebrowser.xml
index 0ef85788441..4614deffca8 100644
--- a/tools/data_source/ucsc_tablebrowser.xml
+++ b/tools/data_source/ucsc_tablebrowser.xml
@@ -16,7 +16,7 @@
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
 	    <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" />
 	    <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
-	    <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
+	    <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
 	</request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
diff --git a/tools/data_source/ucsc_tablebrowser_archaea.xml b/tools/data_source/ucsc_tablebrowser_archaea.xml
index 79246a8435b..63a952947cc 100644
--- a/tools/data_source/ucsc_tablebrowser_archaea.xml
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml
@@ -16,7 +16,7 @@
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
         <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
         <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
+        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
     </request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
diff --git a/tools/data_source/ucsc_tablebrowser_test.xml b/tools/data_source/ucsc_tablebrowser_test.xml
index 5a3a7b803fb..d8eddb4066b 100644
--- a/tools/data_source/ucsc_tablebrowser_test.xml
+++ b/tools/data_source/ucsc_tablebrowser_test.xml
@@ -16,7 +16,7 @@
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
         <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
         <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
+        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
     </request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index d6c542f8bf2..99bc7dee46b 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -3,7 +3,8 @@
   <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Convert coordinates of">
-      <validator type="unspecified_build" />
+      <validator type="unspecified_build" />
+      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
     </param>
     <param name="to_dbkey" type="select" label="To">
       <options from_file="liftOver.loc">
@@ -11,7 +12,7 @@
         <column name="value" index="2"/>
         <column name="dbkey" index="0"/>
         <filter type="data_meta" ref="input" key="dbkey" column="0" />
-      </options>
+      </options>
     </param> 
   </inputs>
   <outputs>
@@ -39,11 +40,7 @@ Make sure that the genome build of the input dataset is specified (click the pen
 
 .. class:: warningmark
 
-The **To** list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset. 
-
-.. class:: warningmark
-
-This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case, it will return empty output datasets.
+This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case with any line of the input dataset, the tool will return empty output datasets.
 
 -----
 
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml
index de290900668..34d6bde909b 100644
--- a/tools/extract/phastOdds/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_tool.xml
@@ -4,6 +4,7 @@
   <inputs>
     <param format="interval" name="input" type="data" label="Interval file">
       <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."/>
+      <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
     </param>
     <param name="score_file" type="select" label="Available datasets">
       <options from_file="phastOdds.loc">
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml
index d6f3f8bc847..14535ae3189 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml
@@ -8,6 +8,8 @@
   <inputs>
     <param format="interval" name="input1" type="data" label="Interval file">
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/>
+      <validator type="dataset_metadata_in_file" filename="binned_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build." />
+      
     </param>
     <conditional name="score_source_type">
       <param name="score_source" type="select" label="Score Source">