diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index bbb817e8a67..e8b598fe639 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -25,6 +25,7 @@ class Configuration( object ):
         self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root )
         self.database_connection =  kwargs.get( "database_connection", False )
         self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
+        self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
         self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root )
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 68582a8d4b7..deca35fd6a2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -286,6 +286,10 @@ class JobWrapper( object ):
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
         param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         param_dict = self.tool.params_from_strings( param_dict, self.app )
+        # Create generated output children and primary datasets and add to param_dict
+        collected_datasets = {'children':self.tool.collect_child_datasets(out_data),'primary':self.tool.collect_primary_datasets(out_data)}
+        param_dict.update({'__collected_datasets__':collected_datasets})
+        # Call 'exec_after_process' hook
         self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data, 
                              out_data=out_data, param_dict=param_dict, 
                              tool=self.tool, stdout=stdout, stderr=stderr )
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 96ef9d6f873..db0b7f59644 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -143,7 +143,7 @@ class Dataset( object ):
     engine = None
     def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, 
                   dbkey=None, state=None, metadata=None, history=None, parent_id=None, designation=None,
-                  validation_errors=None ):
+                  validation_errors=None, visible=True ):
         self.name = name or "Unnamed dataset"
         self.id = id
         self.hid = hid
@@ -158,6 +158,7 @@ class Dataset( object ):
         self.designation = designation
         self.deleted = False
         self.purged = False
+        self.visible = visible
         # Relationships
         self.history = history
         self.validation_errors = validation_errors
@@ -267,9 +268,9 @@ class Dataset( object ):
         #         if data.parent_id and data.parent_id == self.id:
         #             if designation == data.designation:
         #                 return data
-        for child_assocation in self.children:
+        for child_association in self.children:
             if child_association.designation == designation:
-                return child
+                return child_association.child
         return None
     def purge( self ):
         """Removes the file contents from disk """
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index d38bc1e0597..b8b9c43e0c4 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -73,6 +73,7 @@ Dataset.table = Table( "dataset", metadata,
     Column( "designation", TrimmedString( 255 ) ),
     Column( "deleted", Boolean ),
     Column( "purged", Boolean ),
+    Column( "visible", Boolean ),
     ForeignKeyConstraint(['parent_id'],['dataset.id'], ondelete="CASCADE") )
 
 ValidationError.table = Table( "validation_error", metadata,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 99e2492d6ce..c2239c4bd7c 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -6,7 +6,7 @@ import pkg_resources;
 pkg_resources.require( "Cheetah" )
 pkg_resources.require( "simplejson" )
 
-import logging, os, string, sys, tempfile
+import logging, os, string, sys, tempfile, glob, shutil
 import simplejson
 import sha, hmac, binascii
 
@@ -782,7 +782,10 @@ class Tool:
                 child = child_association.child
                 key = "_CHILD___%s___%s" % ( name, child.designation ) 
                 param_dict[ key ] = DatasetFilenameWrapper( child )
-        # Return the dictionary of parameters        
+        # We add access to app here, this allows access to app.config, etc
+        param_dict['__app__'] = RawObjectWrapper( self.app )
+        param_dict['__new_file_path__'] = self.app.config.new_file_path #More convienent access to this value; we don't need to wrap a string
+        # Return the dictionary of parameters
         return param_dict
     
     def build_param_file( self, param_dict, directory=None ):
@@ -859,12 +862,90 @@ class Tool:
             e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) )
             raise 
         
+    def collect_child_datasets( self, output):
+        children = {}
+        #Loop through output file names, looking for generated children in form of 'child_parentId_designation_visibility_extension'
+        for name, outdata in output.items():
+            for filename in glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ):
+                if not name in children:
+                    children[name] = {}
+                fields = os.path.basename(filename).split("_")
+                fields.pop(0)
+                parent_id = int(fields.pop(0))
+                designation = fields.pop(0)
+                visible = fields.pop(0).lower()
+                if visible == "visible": visible = True
+                else: visible = False
+                ext = fields.pop(0).lower()
+                # Create new child dataset
+                child_data = self.app.model.Dataset(extension=ext, parent_id=parent_id, designation=designation, visible=visible, dbkey=outdata.dbkey)
+                child_data.flush()
+                # Move data from temp location to dataset location
+                shutil.move(filename, child_data.file_name)
+                child_data.name = "Secondary Dataset (%s)" % (designation)
+                child_data.state = child_data.states.OK
+                child_data.init_meta()
+                child_data.set_peek()
+                child_data.flush()
+                # Add to child accociation table
+                assoc = self.app.model.DatasetChildAssociation()
+                assoc.child = child_data
+                assoc.designation = child_data.designation
+                outdata.children.append( assoc )
+                # Add child to return dict 
+                children[name][designation] = child_data
+        return children
+        
+    def collect_primary_datasets( self, output):
+        primary_datasets = {}
+        #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension'
+        for name, outdata in output.items():
+            for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ):
+                if not name in primary_datasets:
+                    primary_datasets[name] = {}
+                fields = os.path.basename(filename).split("_")
+                fields.pop(0)
+                parent_id = int(fields.pop(0))
+                designation = fields.pop(0)
+                visible = fields.pop(0).lower()
+                if visible == "visible": visible = True
+                else: visible = False
+                ext = fields.pop(0).lower()
+                # Create new primary dataset
+                primary_data = self.app.model.Dataset(extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey)
+                primary_data.flush()
+                self.app.model.History.get(outdata.history_id).add_dataset(primary_data)
+                # Move data from temp location to dataset location
+                shutil.move(filename, primary_data.file_name)
+                primary_data.name = outdata.name
+                primary_data.info = outdata.info
+                primary_data.state = primary_data.states.OK
+                primary_data.init_meta(copy_from=outdata)
+                primary_data.set_peek()
+                primary_data.flush()
+                # Add dataset to return dict 
+                primary_datasets[name][designation] = primary_data
+        return primary_datasets
+
+        
 # ---- Utility classes to be factored out -----------------------------------
         
 class BadValue( object ):
     def __init__( self, value ):
         self.value = value
         
+
+class RawObjectWrapper( object ):
+    """
+    Wraps an object so that __str__ returns module_name:class_name.
+    """
+    def __init__( self, obj ):
+        self.obj = obj
+    def __str__( self ):
+        return "%s:%s" % (self.obj.__module__, self.obj.__class__.__name__)
+    def __getattr__( self, key ):
+        return getattr( self.obj, key )
+
 class InputValueWrapper( object ):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.
diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index e9d10606098..ca29fd0574a 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -122,6 +122,21 @@ class Universe( BaseController ):
         else:
             return "No data with id=%d" % id
 
+    @web.expose
+    def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"):
+        """
+        Returns child data directly into the browser, based upon parent_id and designation.
+        """
+        try:
+            data = self.app.model.Dataset.get( parent_id )
+            if data:
+                child = data.get_child_by_designation(designation)
+                if child:
+                    return self.display(trans, id=child.id, tofile=tofile, toext=toext)
+        except Exception:
+            pass
+        return "A child named %s could not be found for data %s" % ( designation, parent_id )
+
     @web.expose
     def display_as( self, trans, id=None, display_app=None, **kwd ):
         """Returns a file in a format that can successfully be displayed in display_app"""
diff --git a/templates/history.tmpl b/templates/history.tmpl
index 44ab9e72eea..d795c5d3fcf 100644
--- a/templates/history.tmpl
+++ b/templates/history.tmpl
@@ -257,7 +257,7 @@ div#footer {
                 <div> 
                     #if $data.has_data:
                         <a href="display?id=$data.id&tofile=yes&toext=$data.ext" target="_blank">save</a>
-                    	#for $display_app in $data.datatype.get_display_types():
+                        #for $display_app in $data.datatype.get_display_types():
                             #set $display_links = $data.datatype.get_display_links($data, $display_app, $app, $request.base)
                             #if $len($display_links) > 0:
                                 | $data.datatype.get_display_label($display_app)
@@ -276,18 +276,25 @@ div#footer {
             ##  
             ## Child datasets
             ## 
-                              
+            
             #if $len( $data.children ) > 0:
-                <div>
-                    There are ${len( $data.children )} secondary datasets.
-                    #for $idx, $child_assoc in $enumerate($data.children)
-							#set $child = $child_assoc.child
-							$render_dataset( $child, $idx + 1 )
-					#end for
-				</div>
-			#end if
-							    
-	    </div>
+                #set $children = []
+                #for $child_assoc in $data.children:
+                    #if $child_assoc.child.visible:
+                        $children.append($child_assoc.child)
+                    #end if
+                #end for
+                #if $len( $children ) > 0:
+                    <div>
+                        There are ${len( $children )} secondary datasets.
+                        #for $idx, $child in $enumerate($children)
+                            $render_dataset( $child, $idx + 1 )
+                        #end for
+                    </div>
+                #end if
+            #end if
+                                
+        </div>
     </div>
 
 #end def
@@ -299,7 +306,9 @@ div#footer {
 #else    
     ## Render all active (not deleted) datasets, ordered from newest to oldest
     #for $data in reversed( $history.active_datasets )
-        $render_dataset( $data, $data.hid )
+        #if $data.visible:
+            $render_dataset( $data, $data.hid )
+        #end if
     #end for
 #end if
 
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index b246b2bee7a..82a52eed4da 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -29,6 +29,8 @@ database_file = database/universe.sqlite
 
 # Where dataset files are saved
 file_path = database/files
+# Temporary storage for additional datasets, this should be shared through the cluster
+new_file_path = database/tmp
 
 # Tools
 tool_config_file = tool_conf.xml