diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 53a8bca7ba0..8661bfa0832 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -84,7 +84,7 @@ class Data( object ):
         # flag the object as modified for SQLAlchemy.
         if copy_from:
             dataset.metadata = copy_from.metadata
-    def set_meta( self, dataset, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         """Unimplemented method, allows guessing of metadata from contents of file"""
         return True
     def set_readonly_meta( self, dataset ):
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 97d82f1266b..afbb8831ac5 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -64,8 +64,8 @@ class Interval( Tabular ):
         else:
             dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
     
-    def set_meta( self, dataset, first_line_is_header=False, **kwd ):
-        Tabular.set_meta( self, dataset, skip=0 )
+    def set_meta( self, dataset, overwrite = True, first_line_is_header = False, **kwd ):
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 0 )
         
         """Tries to guess from the line the location number of the column for the chromosome, region start-end and strand"""
         if dataset.has_data():
@@ -80,7 +80,8 @@ class Interval( Tabular ):
                         for index, col_name in enumerate( elems ):
                             if col_name in valid:
                                 meta_name = valid[col_name]
-                                setattr( dataset.metadata, meta_name, index+1 )
+                                if overwrite or not dataset.metadata.element_is_set( meta_name ):
+                                    setattr( dataset.metadata, meta_name, index+1 )
                                 values = alias_spec[ meta_name ]
                                 start = values.index( col_name )
                                 for lower in values[ start: ]:
@@ -94,26 +95,32 @@ class Interval( Tabular ):
                         if len( elems ) > 2:
                             for str in data.col1_startswith:
                                 if line.lower().startswith( str ):
-                                    dataset.metadata.chromCol = 1
+                                    if overwrite or not dataset.metadata.element_is_set( 'chromCol' ):
+                                        dataset.metadata.chromCol = 1
                                     try:
                                         int( elems[1] )
-                                        dataset.metadata.startCol = 2
+                                        if overwrite or not dataset.metadata.element_is_set( 'startCol' ):
+                                            dataset.metadata.startCol = 2
                                     except:
                                         pass # Metadata default will be used
                                     try:
                                         int( elems[2] )
-                                        dataset.metadata.endCol = 3
+                                        if overwrite or not dataset.metadata.element_is_set( 'endCol' ):
+                                            dataset.metadata.endCol = 3
                                     except:
                                         pass # Metadata default will be used
                                     if len( elems ) > 3:
                                         try:
                                             int( elems[3] )
                                         except:
-                                            dataset.metadata.nameCol = 4 
+                                            if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
+                                                dataset.metadata.nameCol = 4 
                                     if len( elems ) < 6 or elems[5] not in data.valid_strand:
-                                        dataset.metadata.strandCol = 0
+                                        if overwrite or not dataset.metadata.element_is_set(  'strandCol' ):
+                                            dataset.metadata.strandCol = 0
                                     else:
-                                        dataset.metadata.strandCol = 6
+                                        if overwrite or not dataset.metadata.element_is_set( 'strandCol' ):
+                                            dataset.metadata.strandCol = 6
                                     metadata_is_set = True
                                     break
                         if metadata_is_set:
@@ -286,8 +293,9 @@ class Bed( Interval ):
     MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter )
     MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )
     MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
+    ###do we need to repeat these? they are the same as should be inherited from interval type
     
-    def set_meta( self, dataset, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         """Sets the metadata information for datasets previously determined to be in bed format."""
         i = 0
         if dataset.has_data():
@@ -300,15 +308,18 @@ class Bed( Interval ):
                         for startswith in data.col1_startswith:
                             if line.lower().startswith( startswith ):
                                 if len( elems ) > 3:
-                                    dataset.metadata.nameCol = 4
+                                    if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
+                                        dataset.metadata.nameCol = 4
                                 if len(elems) < 6:
-                                    dataset.metadata.strandCol = 0
+                                    if overwrite or not dataset.metadata.element_is_set( 'strandCol' ):
+                                        dataset.metadata.strandCol = 0
                                 else:
-                                    dataset.metadata.strandCol = 6
+                                    if overwrite or not dataset.metadata.element_is_set( 'strandCol' ):
+                                        dataset.metadata.strandCol = 6
                                 metadata_set = True
                                 break
                 if metadata_set: break
-            Tabular.set_meta( self, dataset, skip=i )
+            Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )
     
     def as_ucsc_display_file( self, dataset, **kwd ):
         """Returns file contents with only the bed data. If bed 6+, treat as interval."""
@@ -443,7 +454,7 @@ class Gff( Tabular ):
         Tabular.__init__(self, **kwd)
         self.add_display_app ( 'elegans', 'display in GBrowse', 'as_gbrowse_display_file', 'gbrowse_links' )
 
-    def set_meta( self, dataset, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         i = 0
         for i, line in enumerate( file ( dataset.file_name ) ):
             line = line.rstrip('\r\n')
@@ -456,7 +467,7 @@ class Gff( Tabular ):
                         break
                     except:
                         pass
-        Tabular.set_meta( self, dataset, skip=i )
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )
 
     def make_html_table( self, dataset, skipchars=[] ):
         """Create HTML table, used for displaying peek"""
@@ -589,7 +600,7 @@ class Gff3( Gff ):
         """Initialize datatype, by adding GBrowse display app"""
         Gff.__init__(self, **kwd)
 
-    def set_meta( self, dataset, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         i = 0
         for i, line in enumerate( file ( dataset.file_name ) ):
             line = line.rstrip('\r\n')
@@ -614,7 +625,7 @@ class Gff3( Gff ):
                     phase = elems[7]
                     if valid_start and valid_end and start < end and strand in self.valid_gff3_strand and phase in self.valid_gff3_phase:
                         break
-        Tabular.set_meta( self, dataset, skip=i )
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )
 
     def sniff( self, filename ):
         """
@@ -692,7 +703,7 @@ class Wiggle( Tabular ):
     def make_html_table( self, dataset ):
         return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
 
-    def set_meta( self, dataset, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         i = 0
         for i, line in enumerate( file ( dataset.file_name ) ):
             line = line.rstrip('\r\n')
@@ -705,7 +716,7 @@ class Wiggle( Tabular ):
                     for str in data.col1_startswith:
                         if elems[0].lower().startswith(str):
                             break
-        Tabular.set_meta( self, dataset, skip=i )
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )
 
     def sniff( self, filename ):
         """
@@ -746,8 +757,8 @@ class CustomTrack ( Tabular ):
         """Initialize interval datatype, by adding UCSC display app"""
         Tabular.__init__(self, **kwd)
         self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' )
-    def set_meta( self, dataset, **kwd ):
-        Tabular.set_meta( self, dataset, skip=1 )
+    def set_meta( self, dataset, overwrite = True, **kwd ):
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 )
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
         return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
@@ -858,8 +869,8 @@ class GBrowseTrack ( Tabular ):
         Tabular.__init__(self, **kwd)
         self.add_display_app ('elegans', 'display in GBrowse', 'as_gbrowse_display_file', 'gbrowse_links' )
 
-    def set_meta( self, dataset, **kwd ):
-        Tabular.set_meta( self, dataset, skip=1 )
+    def set_meta( self, dataset, overwrite = True, **kwd ):
+        Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 )
     
     def make_html_table( self, dataset ):
         return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index 6aea93dd336..05ee719c6c9 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -185,6 +185,8 @@ class MetadataCollection:
             self.parent._metadata = value
         else:
             self.bunch[name] = value
+    def element_is_set( self, name ):
+        return bool( self.bunch.get( name, False ) )
 
 MetadataElement = Statement(MetadataElementSpec)
 
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 4efa3da5922..954ee426f98 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -190,8 +190,7 @@ class Registry( object ):
         # initialization.
         if data.has_data():
             data.init_meta( copy_from=data )
-            if isinstance( data.datatype, tabular.Tabular ):
-                data.set_readonly_meta()
+            data.set_meta( overwrite = False )
             data.set_peek()
         return data
 
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 997714a59c0..a6ca0db0136 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -164,7 +164,7 @@ class Maf( Alignment ):
     def init_meta( self, dataset, copy_from=None ):
         Alignment.init_meta( self, dataset, copy_from=copy_from )
     
-    def set_meta( self, dataset, first_line_is_header=False, **kwd ):
+    def set_meta( self, dataset, overwrite = True, **kwd ):
         """
         Parses and sets species and chromosomes from MAF files.
         """
@@ -190,6 +190,7 @@ class Maf( Alignment ):
                 if i > 100000: break
         except: 
             pass
+        #these metadata values are not accessable by users, always overwrite
         dataset.metadata.species = species
         dataset.metadata.species_chromosomes = species_chromosomes
     
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index fddd92de944..6d0b2e73deb 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -26,8 +26,8 @@ class Tabular( data.Text ):
         data.Text.init_meta( self, dataset, copy_from=copy_from )
     def set_readonly_meta( self, dataset, skip=1, **kwd ):
         """Resets the values of readonly metadata elements."""
-        Tabular.set_meta( self, dataset, skip=skip )
-    def set_meta( self, dataset, skip=1, **kwd ):
+        Tabular.set_meta( self, dataset, overwrite = True, skip = skip )
+    def set_meta( self, dataset, overwrite = True, skip = 1, **kwd ):
         """
         Tries to determine the number of columns as well as those columns
         that contain numerical values in the dataset.  A skip parameter is
@@ -35,6 +35,7 @@ class Tabular( data.Text ):
         their data type classes are responsible to determine how many invalid
         comment lines should be skipped.
         """
+        #we treat 'overwrite' as always True (we always want to set tabular metadata when called)
         if dataset.has_data():
             column_types = []
  
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index a53dddd0d7b..3cda6ce6c76 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -409,12 +409,7 @@ class JobWrapper( object ):
                     dataset.blurb = "error"
                 elif dataset.has_data():
                     # Only set metadata values if they are missing...
-                    if dataset.missing_meta():
-                        dataset.set_meta()
-                    else:
-                        # ...however, some tools add / remove columns,
-                        # so we have to reset the readonly metadata values
-                        dataset.set_readonly_meta()
+                    dataset.set_meta( overwrite_exisiting = False )
                     dataset.set_peek()
                 else:
                     dataset.blurb = "empty"
diff --git a/scripts/check_galaxy.py b/scripts/check_galaxy.py
index 572b22388b9..faf9df58e6b 100755
--- a/scripts/check_galaxy.py
+++ b/scripts/check_galaxy.py
@@ -190,7 +190,7 @@ class Browser:
         tc.fv("1", "password", pw)
         tc.submit("Login")
         tc.code(200)
-        if len(tc.get_browser()._browser.forms()) > 0:
+        if len(tc.get_browser().get_all_forms()) > 0:
             # uh ohs, fail
             p = userParser()
             p.feed(tc.browser.get_html())
@@ -210,7 +210,7 @@ class Browser:
         tc.fv("1", "confirm", pw)
         tc.submit("Create")
         tc.code(200)
-        if len(tc.get_browser()._browser.forms()) > 0:
+        if len(tc.get_browser().get_all_forms()) > 0:
             p = userParser()
             p.feed(tc.browser.get_html())
             if p.already_exists: