Add a SelectToolParameterWrapper object and a wrap method to Tool.execute() that allows for things like the following in tool configs:

<outputs>
  <data format="input" name="output" label="Blat on {<input_param>.value_label}" />
</outputs>

Also replace EOL chars with <br> in a tool's output data.info so that they are displayed in HTML.

lib/galaxy/datatypes/data.py

@@ -132,7 +132,8 @@ class Data( object ):
     def display_info(self, dataset):
         """Returns formated html of dataset info"""
         try:
-            return escape(dataset.info)
+            # Change new line chars to html
+            return escape( dataset.info ).replace( "\r", "\n" ).replace( "\n", "<br>" )
         except:
             return "info unavailable"
     def validate(self, dataset):

lib/galaxy/tools/__init__.py

@@ -1072,10 +1072,11 @@ class Tool:
                                                 datatypes_registry = self.app.datatypes_registry,
                                                 tool = self,
                                                 name = input.name )
+                elif isinstance( input, SelectToolParameter ):
+                    input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app )
                 else:
-                    input_values[ input.name ] = \
-                        InputValueWrapper( input, input_values[ input.name ], param_dict )
-        # HACK: only wrap if check_values is false, this deals with external
+                    input_values[ input.name ] = InputValueWrapper( input, input_values[ input.name ], param_dict )
+        # HACK: only wrap if check_values is not false, this deals with external
         #       tools where the inputs don't even get passed through. These
         #       tools (e.g. UCSC) should really be handled in a special way.
         if self.check_values:
@@ -1416,7 +1417,21 @@ class InputValueWrapper( object ):
         return self.input.to_param_dict_string( self.value, self._other_values )
     def __getattr__( self, key ):
         return getattr( self.value, key )
-        
+
+class SelectToolParameterWrapper( object ):
+    """
+    Wraps a SelectTooParameter so that __str__ returns the selected value, but all other
+    attributes are accessible.
+    """
+    def __init__( self, input, value, app ):
+        self.input = input
+        self.value = value
+        self.input.value_label = input.value_to_display_text( value, app )
+    def __str__( self ):
+        return self.input.to_param_dict_string( self.value )
+    def __getattr__( self, key ):
+        return getattr( self.input, key )
+
 class DatasetFilenameWrapper( object ):
     """
     Wraps a dataset so that __str__ returns the filename, but all other

lib/galaxy/tools/actions/__init__.py

@@ -1,9 +1,11 @@
 from galaxy.util.bunch import Bunch
 from galaxy.tools.parameters import *
+from galaxy.tools.parameters.grouping import *
 from galaxy.util.template import fill_template
 from galaxy.util.none_like import NoneDataset
 from galaxy.web import url_for
 from galaxy.jobs import JOB_OK
+import galaxy.tools
 
 import logging
 log = logging.getLogger( __name__ )
@@ -65,6 +67,26 @@ class DefaultToolAction( object ):
         return input_datasets
     
     def execute(self, tool, trans, incoming={}, set_output_hid=True ):
+        def wrap_values( inputs, input_values ):
+            # Wrap tool inputs as necessary
+            for input in inputs.itervalues():
+                if isinstance( input, Repeat ):
+                    for d in input_values[ input.name ]:
+                        wrap_values( input.inputs, d )
+                elif isinstance( input, Conditional ):
+                    values = input_values[ input.name ]
+                    current = values["__current_case__"]
+                    wrap_values( input.cases[current].inputs, values )
+                elif isinstance( input, DataToolParameter ):
+                    input_values[ input.name ] = \
+                        galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ],
+                                                             datatypes_registry = trans.app.datatypes_registry,
+                                                             tool = tool,
+                                                             name = input.name )
+                elif isinstance( input, SelectToolParameter ):
+                    input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app )
+                else:
+                    input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming )
         out_data = {}
         # Collect any input datasets from the incoming parameters
         inp_data = self.collect_input_datasets( tool, incoming, trans )
@@ -151,6 +173,11 @@ class DefaultToolAction( object ):
             # Set output label
             if output.label:
                 params = dict( incoming )
+                # wrapping the params allows the tool config to contain things like
+                # <outputs>
+                #     <data format="input" name="output" label="Blat on ${<input_param>.name}" />
+                # </outputs>
+                wrap_values( tool.inputs, params )
                 params['tool'] = tool
                 params['on_string'] = on_text
                 data.name = fill_template( output.label, context=params )