diff --git a/client/galaxy/scripts/mvc/app/app-analysis.js b/client/galaxy/scripts/mvc/app/app-analysis.js
index 97abe312d96..ef355741813 100644
--- a/client/galaxy/scripts/mvc/app/app-analysis.js
+++ b/client/galaxy/scripts/mvc/app/app-analysis.js
@@ -1,34 +1,38 @@
 define(['utils/utils', 'mvc/tools', 'mvc/upload/upload-view', 'mvc/ui/ui-misc',
-        'mvc/history/options-menu', 'mvc/history/history-panel-edit-current'],
-    function( Utils, Tools, Upload, Ui, optionsMenu, HistoryPanel ) {
+        'mvc/history/options-menu', 'mvc/history/history-panel-edit-current', 'mvc/tools/tools-form'],
+    function( Utils, Tools, Upload, Ui, optionsMenu, HistoryPanel, ToolsForm ) {
 
     /* Builds the center panel */
     var CenterPanel = Backbone.View.extend({
         initialize: function( options ) {
             this.options = Utils.merge( options, {} );
             this.setElement( this._template() );
-            var params = this.options.params;
-            this.$( '#galaxy_main' ).prop( 'src', Galaxy.root + (
-                ( params.tool_id && ( 'tool_runner?' + $.param( params ) ) ) ||
-                ( params.workflow_id && ( 'workflow/run?id=' + params.workflow_id ) ) ||
-                ( params.m_c && ( params.m_c + '/' + params.m_a ) ) ||
-                ( Galaxy.config.require_login && !Galaxy.user.id && 'user/login') ||
-                'root/welcome'
-            ));
             var self = this;
             this.$( '#galaxy_main' ).on( 'load', function() {
-                $( this ).show();
-                self.$( '#center-panel' ).empty().hide();
-                var galaxy_main = this.contentWindow;
-                if ( galaxy_main ) {
+                var location = this.contentWindow && this.contentWindow.location;
+                if ( location && location.host ) {
+                    $( this ).show();
+                    self.$( '#center-panel' ).empty().hide();
                     Galaxy.trigger( 'galaxy_main:load', {
-                        fullpath: galaxy_main.location.pathname + galaxy_main.location.search + galaxy_main.location.hash,
-                        pathname: galaxy_main.location.pathname,
-                        search  : galaxy_main.location.search,
-                        hash    : galaxy_main.location.hash
+                        fullpath: location.pathname + location.search + location.hash,
+                        pathname: location.pathname,
+                        search  : location.search,
+                        hash    : location.hash
                     });
                 }
             });
+            var params = $.extend( {}, Galaxy.params );
+            if ( params.tool_id !== 'upload1' && ( params.tool_id || params.job_id ) ) {
+                params.tool_id && ( params.id = params.tool_id );
+                this.display( ( new ToolsForm.View( params ) ).$el );
+            } else {
+                this.$( '#galaxy_main' ).prop( 'src', Galaxy.root + (
+                    ( params.workflow_id && ( 'workflow/run?id=' + params.workflow_id ) ) ||
+                    ( params.m_c && ( params.m_c + '/' + params.m_a ) ) ||
+                    ( Galaxy.config.require_login && !Galaxy.user.id && 'user/login') ||
+                    'root/welcome'
+                ));
+            }
         },
         display: function( $el ) {
             this.$( '#galaxy_main' ).hide();
@@ -206,4 +210,4 @@ define(['utils/utils', 'mvc/tools', 'mvc/upload/upload-view', 'mvc/ui/ui-misc',
         center  : CenterPanel,
         right   : RightPanel
     }
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/app/app-view.js b/client/galaxy/scripts/mvc/app/app-view.js
index a67e1818eb2..f735b289ac6 100644
--- a/client/galaxy/scripts/mvc/app/app-view.js
+++ b/client/galaxy/scripts/mvc/app/app-view.js
@@ -8,12 +8,17 @@ define(['utils/utils', 'galaxy.masthead', 'galaxy.menu', 'galaxy.frame',
     return Backbone.View.extend({
         initialize: function( options ) {
             this.options = Utils.merge( options, {} );
-            this.params  = this.options.params;
             this.setElement( this._template( options ) );
 
             // register this view
             Galaxy.app = this;
 
+            // url request parameters
+            Galaxy.params = this.options.params;
+
+            // shared backbone router
+            Galaxy.router = new Backbone.Router();
+
             // configure body
             $( 'body' ).append( this.$el );
             ensure_dd_helper();
@@ -131,4 +136,4 @@ define(['utils/utils', 'galaxy.masthead', 'galaxy.menu', 'galaxy.frame',
                     '</div>';
         }
     });
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index f62a2fbe616..ae2ab755e2f 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -100,14 +100,11 @@ define([], function() {
         /** Main Template
         */
         _template: function(options) {
-            // create table element
-            var tmp =   '<div class="ui-table-form-element">' +
+            var tmp =   '<div class="ui-table-form-element input-name-' + options.name + '">' +
                             '<div class="ui-table-form-error ui-error">' +
                                 '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' +
                             '</div>' +
                             '<div class="ui-table-form-title">';
-
-            // is optional
             if (options.collapsible) {
                 tmp +=          '<div class="ui-table-form-optional">' +
                                     '<i class="icon"/>' + options.label +
@@ -115,12 +112,8 @@ define([], function() {
             } else {
                 tmp += options.label;
             }
-
-            // finalize title
             tmp +=          '</div>' +
                             '<div class="ui-table-form-field">';
-
-            // add help
             tmp +=              '<div class="ui-table-form-info">';
             if (options.help) {
                 tmp +=              options.help;
@@ -129,13 +122,9 @@ define([], function() {
                 }
             }
             tmp +=              '</div>';
-
-            // finalize
             tmp +=          '</div>' +
                         '</div>';
-
-            // return input element
             return tmp;
         }
     });
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js
index c4a344e58ca..f306604d0ca 100644
--- a/client/galaxy/scripts/mvc/form/form-section.js
+++ b/client/galaxy/scripts/mvc/form/form-section.js
@@ -316,6 +316,7 @@ define(['utils/utils',
 
             // create input field wrapper
             var input_element = new InputElement(this.app, {
+                name                : input_def.name,
                 label               : input_def.label || input_def.name,
                 value               : input_def.value,
                 default_value       : input_def.default_value,
@@ -348,4 +349,4 @@ define(['utils/utils',
     return {
         View: View
     };
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js
index c6ea1a61624..add567a665c 100644
--- a/client/galaxy/scripts/mvc/form/form-view.js
+++ b/client/galaxy/scripts/mvc/form/form-view.js
@@ -206,12 +206,8 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                 inputs : this.options.inputs
             });
 
-            // switch to classic tool form mako if the form definition is incompatible
-            if (this.incompatible) {
-                this.$el.hide();
-                $('#tool-form-classic').show();
-                return;
-            }
+            // remove tooltips
+            $( '.tooltip' ).remove();
 
             // create portlet
             this.portlet = new Portlet.View({
@@ -245,4 +241,4 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
             console.debug('tools-form-base::initialize() - Completed.');
         }
     });
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/tools.js b/client/galaxy/scripts/mvc/tools.js
index 0e37c110738..5c6c9de11e1 100644
--- a/client/galaxy/scripts/mvc/tools.js
+++ b/client/galaxy/scripts/mvc/tools.js
@@ -525,7 +525,7 @@ var ToolLinkView = BaseView.extend({
         }
 
         // regular tools
-        if (this.model.get('model_class') === 'Tool') {
+        if ( this.model.id !== 'upload1' && this.model.get( 'model_class' ) === 'Tool' ) {
             var self = this;
             $link.find('a').on('click', function(e) {
                 e.preventDefault();
diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js
index 5f4406d5bc2..056ea51a774 100644
--- a/client/galaxy/scripts/mvc/tools/tools-form-base.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js
@@ -44,6 +44,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                 }
             }, this.options);
 
+            // allow option customization
+            this.options.customize && this.options.customize( this.options );
+
             // create form
             this.form = new Form(this.options);
 
@@ -65,20 +68,19 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             this.options.id = options.id;
             this.options.version = options.version;
 
-            if (options.job_id) {
+            if ( options.job_id ) {
                 build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';
             } else {
-                // construct url
                 var build_url = Galaxy.root + 'api/tools/' + options.id + '/build?';
-                if (options.dataset_id) {
-                    build_url += 'dataset_id=' + options.dataset_id;
-                } else {
+                if ( options.version ) {
                     build_url += 'tool_version=' + options.version + '&';
-                    var loc = top.location.href;
-                    var pos = loc.indexOf('?');
-                    if (loc.indexOf('tool_id=') != -1 && pos !== -1) {
-                        build_url += loc.slice(pos + 1);
-                    }
+                }
+                if ( Galaxy.params && Galaxy.params.tool_id == options.id ) {
+                    _.each( Galaxy.params, function ( item, key ) {
+                        if ( [ 'tool_version', 'tool_id' ].indexOf( key ) == -1 ) {
+                            build_url += key + '=' + item + '&';
+                        }
+                    } );
                 }
             }
 
@@ -117,18 +119,24 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
 
                     // show error
                     var error_message = response.error || response.err_msg || 'Uncaught error.';
-                    if (self.form == undefined){
-                        self.form = new Form();
-                    }
-                    Galaxy.modal.show({
-                        title   : 'Tool cannot be executed',
-                        body    : error_message,
-                        buttons : {
-                            'Close' : function() {
-                                Galaxy.modal.hide();
+                    if ( self.$el.is(':empty') ) {
+                        self.$el.prepend((new Ui.Message({
+                            message     : error_message,
+                            status      : 'danger',
+                            persistent  : true,
+                            large       : true
+                        })).$el);
+                    } else {
+                        Galaxy.modal.show({
+                            title   : 'Tool request failed',
+                            body    : error_message,
+                            buttons : {
+                                'Close' : function() {
+                                    Galaxy.modal.hide();
+                                }
                             }
-                        }
-                    });
+                        });
+                    }
                 }
             });
         },
@@ -350,4 +358,4 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             }
         }
     });
-});
+});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/tools/tools-form.js b/client/galaxy/scripts/mvc/tools/tools-form.js
index 18cd16d75d4..b6257d9aa7a 100644
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -2,50 +2,46 @@
     This is the regular tool form.
 */
 define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tools/tools-form-base', 'mvc/tools/tools-jobs'],
-    function(Utils, Ui, ToolFormBase, ToolJobs) {
-
-    // create form view
+    function( Utils, Ui, ToolFormBase, ToolJobs ) {
     var View = ToolFormBase.extend({
-        // initialize
-        initialize: function(options) {
-            // execute button
+        initialize: function( options ) {
             var self = this;
-            var execute = new Ui.Button({
-                icon     : 'fa-check',
-                tooltip  : 'Execute: ' + options.name,
-                title    : 'Execute',
-                cls      : 'btn btn-primary',
-                floating : 'clear',
-                onclick  : function() {
-                    execute.wait();
-                    self.form.portlet.disable();
-                    ToolJobs.submit(self.form, self.options, function() {
-                        execute.unwait();
-                        self.form.portlet.enable();
-                    });
+            ToolFormBase.prototype.initialize.call( this, Utils.merge({
+                customize       : function( options ) {
+                    // build execute button
+                    options.buttons = {
+                        execute : execute_btn = new Ui.Button({
+                            icon     : 'fa-check',
+                            tooltip  : 'Execute: ' + options.name + ' (' + options.version + ')',
+                            title    : 'Execute',
+                            cls      : 'btn btn-primary',
+                            floating : 'clear',
+                            onclick  : function() {
+                                execute_btn.wait();
+                                self.form.portlet.disable();
+                                ToolJobs.submit( self.form, options, function() {
+                                    execute_btn.unwait();
+                                    self.form.portlet.enable();
+                                } );
+                            }
+                        })
+                    };
+
+                    // remap feature
+                    if ( options.job_id && options.job_remap ) {
+                        options.inputs[ 'rerun_remap_job_id' ] = {
+                            label       : 'Resume dependencies from this job',
+                            name        : 'rerun_remap_job_id',
+                            type        : 'select',
+                            display     : 'radio',
+                            ignore      : '__ignore__',
+                            value       : '__ignore__',
+                            options     : [ [ 'Yes', options.job_id ], [ 'No', '__ignore__' ] ],
+                            help        : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'
+                        }
+                    }
                 }
-            });
-            // add remap button
-            if (options.job_id && options.job_remap) {
-                options.inputs['rerun_remap_job_id'] = {
-                    label       : 'Resume dependencies from this job',
-                    name        : 'rerun_remap_job_id',
-                    type        : 'select',
-                    display     : 'radio',
-                    ignore      : '__ignore__',
-                    value       : '__ignore__',
-                    options     : [['Yes', options.job_id], ['No', '__ignore__']],
-                    help        : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'
-                }
-            }
-            // create options dictionary
-            options = Utils.merge(options, {
-                buttons        : {
-                    execute : execute
-                },
-                initial_errors : true
-            });
-            ToolFormBase.prototype.initialize.call(this, options);
+            }, options ) );
         }
     });
 
diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js
index bfa3709525c..3e64d501b45 100644
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -97,12 +97,11 @@ define(['utils/utils',
         // update
         update: function(options) {
             // get options
-            this.options = Utils.merge(options, this.optionsDefault);
+            this.options = Utils.merge(options, this.options);
 
             // show message
             if (options.message != '') {
                 this.$el.html(this._template(this.options));
-                this.$el.find('.alert').append(options.message);
                 this.$el.fadeIn();
 
                 // clear previous timeouts
@@ -128,7 +127,15 @@ define(['utils/utils',
 
         // template
         _template: function(options) {
-            return '<div class="ui-message alert alert-' + options.status + '"/>';
+            var cls_status = 'ui-message alert alert-' + options.status;
+            if (options.large) {
+                cls_status = ( ( options.status == 'success' && 'done' ) ||
+                               ( options.status == 'danger' && 'error' ) ||
+                                 options.status ) + 'messagelarge';
+            }
+            return  '<div class="' + cls_status + '" >' +
+                        options.message +
+                    '</div>';
         }
     });
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3f2981fd0de..061f060a527 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -451,7 +451,7 @@ class Tool( object, Dictifiable ):
     requires_setting_metadata = True
     default_tool_action = DefaultToolAction
     dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' )
-    default_template = 'tool_form.mako'
+    default_template = ''
 
     def __init__( self, config_file, tool_source, app, guid=None, repository_id=None, allow_code_files=True ):
         """Load a tool from the config named by `config_file`"""
@@ -2330,15 +2330,11 @@ class Tool( object, Dictifiable ):
 
         return tool_dict
 
-    def to_json(self, trans, kwd={}, is_workflow=False):
+    def to_json(self, trans, kwd={}, job=None, is_workflow=False):
         """
         Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
         """
-        job_id = kwd.get('__job_id__', None)
-        dataset_id = kwd.get('__dataset_id__', None)
         history_id = kwd.get('history_id', None)
-
-        # history id
         history = None
         try:
             if history_id is not None:
@@ -2353,34 +2349,6 @@ class Tool( object, Dictifiable ):
             log.exception('tools::to_json - %s.' % error)
             return { 'error': error }
 
-        # load job details if provided
-        job = None
-        if job_id:
-            try:
-                job_id = trans.security.decode_id( job_id )
-                job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
-            except Exception, exception:
-                trans.response.status = 500
-                log.error('Failed to retrieve job.')
-                return { 'error': 'Failed to retrieve job.' }
-        elif dataset_id:
-            try:
-                dataset_id = trans.security.decode_id( dataset_id )
-                data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
-                if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ):
-                    trans.response.status = 500
-                    log.error('User has no access to dataset.')
-                    return { 'error': 'User has no access to dataset.' }
-                job = data.creating_job
-                if not job:
-                    trans.response.status = 500
-                    log.error('Creating job not found.')
-                    return { 'error': 'Creating job not found.' }
-            except Exception, exception:
-                trans.response.status = 500
-                log.error('Failed to get job information.')
-                return { 'error': 'Failed to get job information.' }
-
         # load job parameters into incoming
         tool_message = ''
         if job:
@@ -2670,6 +2638,7 @@ class Tool( object, Dictifiable ):
 
         # add additional properties
         tool_model.update({
+            'id'            : self.id,
             'help'          : tool_help,
             'citations'     : tool_citations,
             'biostar_url'   : trans.app.config.biostar_url,
@@ -2679,7 +2648,9 @@ class Tool( object, Dictifiable ):
             'requirements'  : tool_requirements,
             'errors'        : state_errors,
             'state_inputs'  : state_inputs,
-            'job_remap'     : self._get_job_remap(job)
+            'job_id'        : trans.security.encode_id( job.id ) if job else None,
+            'job_remap'     : self._get_job_remap( job ),
+            'history_id'    : trans.security.encode_id( history.id )
         })
 
         # check for errors
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 0bb5c690fa6..f7ac3c2431b 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -204,12 +204,10 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
         job = self.__get_job(trans, id)
         if not job:
             raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id)
-        tool_id = job.tool_id
-        tool_version = job.tool_version
-        tool = self.app.toolbox.get_tool( tool_id, tool_version )
+        tool = self.app.toolbox.get_tool( job.tool_id, job.tool_version )
         if not tool.is_workflow_compatible:
-            raise exceptions.ConfigDoesNotAllowException( "Tool '%s' cannot be rerun." % ( tool_id ) )
-        return tool.to_json(trans, kwd={'__job_id__' : id})
+            raise exceptions.ConfigDoesNotAllowException( "Tool '%s' cannot be rerun." % ( job.tool_id ) )
+        return tool.to_json(trans, {}, job=job)
 
     def __dictify_associations( self, trans, *association_lists ):
         rval = []
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index 63c2d478611..8a71d7b79f6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -12,13 +12,7 @@ from galaxy import web
 from galaxy.tools import DefaultToolState
 from galaxy.tools import DataSourceTool
 from galaxy.tools.actions import upload_common
-from galaxy.tools.parameters import params_to_incoming
-from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter
-from galaxy.tools.parameters.basic import DataCollectionToolParameter
-from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.util.bunch import Bunch
-from galaxy.util.hash_util import is_hashable
 from galaxy.web import error, url_for
 from galaxy.web.base.controller import BaseUIController
 
@@ -59,15 +53,7 @@ class ToolRunner( BaseUIController ):
         # No tool id passed, redirect to main page
         if tool_id is None:
             return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
-        # When the tool form is initially loaded, the received kwd will not include a 'refresh'
-        # entry (which only is included when another option is selected in the tool_version_select_field),
-        # so the default selected option should be the most recent version of the tool.  The following
-        # check will mae sure this occurs.
-        refreshed_on_change = kwd.get( 'refresh', False )
-        tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
-                                                                             tool_version=None,
-                                                                             get_loaded_tools_by_lineage=False,
-                                                                             set_selected=refreshed_on_change )
+        tool_version_select_field, tools, tool = self.__get_tool_components( tool_id )
         # No tool matching the tool id, display an error (shouldn't happen)
         if not tool or not tool.allow_user_access( trans.user ):
             log.error( "index called with tool id '%s' but no such tool exists", tool_id )
@@ -84,6 +70,8 @@ class ToolRunner( BaseUIController ):
                                                           message=message,
                                                           status=status,
                                                           redirect=redirect ) )
+        if tool.tool_type == 'default':
+            return trans.response.send_redirect( url_for( controller="root", tool_id=tool_id ) )
 
         def _validated_params_for( kwd ):
             params = galaxy.util.Params( kwd, sanitize=False )  # Sanitize parameters when substituting into command line via input wrappers
@@ -124,25 +112,14 @@ class ToolRunner( BaseUIController ):
                                     **vars )
 
     @web.expose
-    def rerun( self, trans, id=None, from_noframe=None, job_id=None, **kwd ):
+    def rerun( self, trans, id=None, job_id=None, **kwd ):
         """
         Given a HistoryDatasetAssociation id, find the job and that created
         the dataset, extract the parameters, and display the appropriate tool
         form with parameters already filled in.
         """
-        if job_id:
-            try:
-                job_id = trans.security.decode_id( job_id )
-                job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
-            except:
-                error( "Invalid value for 'job_id' parameter" )
-            if not trans.user_is_admin():
-                for data_assoc in job.output_datasets:
-                    # only allow rerunning if user is allowed access to the dataset.
-                    if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data_assoc.dataset.dataset ):
-                        error( "You are not allowed to rerun this job" )
-            param_error_text = "Failed to get parameters for job id %d " % job_id
-        else:
+
+        if job_id is None:
             if not id:
                 error( "'id' parameter is required" )
             try:
@@ -160,135 +137,11 @@ class ToolRunner( BaseUIController ):
                 error( "You are not allowed to access this dataset" )
             # Get the associated job, if any.
             job = data.creating_job
-            if not job:
-                raise Exception("Failed to get job information for dataset hid %d" % data.hid)
-            param_error_text = "Failed to get parameters for dataset id %d " % data.id
-        # Get the tool object
-        tool_id = job.tool_id
-        tool_version = job.tool_version
-        try:
-            tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
-                                                                                 tool_version=tool_version,
-                                                                                 get_loaded_tools_by_lineage=False,
-                                                                                 set_selected=True )
-            if ( tool.id == job.tool_id or tool.old_id == job.tool_id ) and tool.version == job.tool_version:
-                tool_id_version_message = ''
-            elif tool.id == job.tool_id:
-                if job.tool_version is None:
-                    # For some reason jobs don't always keep track of the tool version.
-                    tool_id_version_message = ''
-                else:
-                    tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available.  ' % job.tool_version
-                    if len( tools ) > 1:
-                        tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
-                    else:
-                        tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
+            if job:
+                job_id = trans.security.encode_id( job.id )
             else:
-                if len( tools ) > 1:
-                    tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available.  ' % job.tool_version
-                    tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
-                else:
-                    tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version )
-                    tool_id_version_message += 'currently available.  You can rerun the job with this tool, which is a derivation of the original tool.'
-            assert tool is not None, 'Requested tool has not been loaded.'
-        except:
-            # This is expected so not an exception.
-            tool_id_version_message = ''
-            error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id )
-        if not tool.allow_user_access( trans.user ):
-            error( "The requested tool is unknown." )
-        # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now
-        if not tool.is_workflow_compatible:
-            error( "The '%s' tool does not currently support rerunning." % tool.name )
-        # Get the job's parameters
-        try:
-            params_objects = job.get_param_values( trans.app, ignore_errors=True )
-        except:
-            raise Exception( param_error_text )
-        upgrade_messages = tool.check_and_update_param_values( params_objects, trans, update_values=False )
-        # Need to remap dataset parameters. Job parameters point to original
-        # dataset used; parameter should be the analygous dataset in the
-        # current history.
-        history = trans.get_history()
-        hda_source_dict = {}  # Mapping from HDA in history to source HDAs.
-        for hda in history.datasets:
-            source_hda = hda.copied_from_history_dataset_association
-            while source_hda:  # should this check library datasets as well?
-                # FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
-                # but is still less than perfect when eg individual datasets are copied between histories
-                if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
-                    hda_source_dict[ source_hda ] = hda
-                source_hda = source_hda.copied_from_history_dataset_association
-        # Ditto for dataset collections.
-        hdca_source_dict = {}
-        for hdca in history.dataset_collections:
-            source_hdca = hdca.copied_from_history_dataset_collection_association
-            while source_hdca:
-                if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
-                    hdca_source_dict[ source_hdca ] = hdca
-                source_hdca = source_hdca.copied_from_history_dataset_collection_association
-
-        # Unpack unvalidated values to strings, they'll be validated when the
-        # form is submitted (this happens when re-running a job that was
-        # initially run by a workflow)
-        # This needs to be done recursively through grouping parameters
-        def rerun_callback( input, value, prefixed_name, prefixed_label ):
-            if isinstance( value, UnvalidatedValue ):
-                try:
-                    return input.to_html_value( value.value, trans.app )
-                except Exception, e:
-                    # Need to determine when (if ever) the to_html_value call could fail.
-                    log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) )
-                    return str( value )
-            if isinstance( input, DataToolParameter ):
-                if isinstance(value, list):
-                    values = []
-                    for val in value:
-                        if is_hashable( val ):
-                            if val in history.datasets:
-                                values.append( val )
-                            elif val in hda_source_dict:
-                                values.append( hda_source_dict[ val ])
-                    return values
-                if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
-                    return hda_source_dict[ value ]
-            elif isinstance( input, DataCollectionToolParameter ):
-                if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict:
-                    return hdca_source_dict[ value ]
-
-        visit_input_values( tool.inputs, params_objects, rerun_callback )
-        # Create a fake tool_state for the tool, with the parameters values
-        state = tool.new_state( trans )
-        state.inputs = params_objects
-        # If the job failed and has dependencies, allow dependency remap
-        if job.state == job.states.ERROR:
-            try:
-                if [ hda.dependent_jobs for hda in [ jtod.dataset for jtod in job.output_datasets ] if hda.dependent_jobs ]:
-                    state.rerun_remap_job_id = trans.app.security.encode_id(job.id)
-            except:
-                # Job has no outputs?
-                pass
-        # create an incoming object from the original job's dataset-modified param objects
-        incoming = {}
-        params_to_incoming( incoming, tool.inputs, params_objects, trans.app )
-        incoming[ "tool_state" ] = galaxy.util.object_to_string( state.encode( tool, trans.app ) )
-        template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages )  # update new state with old parameters
-        # Is the "add frame" stuff neccesary here?
-        add_frame = AddFrameData()
-        add_frame.debug = trans.debug
-        if from_noframe is not None:
-            add_frame.wiki_url = trans.app.config.wiki_url
-            add_frame.from_noframe = True
-        return trans.fill_template( template,
-                                    history=history,
-                                    toolbox=self.get_toolbox(),
-                                    tool_version_select_field=tool_version_select_field,
-                                    tool=tool,
-                                    job=job,
-                                    util=galaxy.util,
-                                    add_frame=add_frame,
-                                    tool_id_version_message=tool_id_version_message,
-                                    **vars )
+                raise Exception("Failed to get job information for dataset hid %d" % data.hid)
+        return trans.response.send_redirect( url_for( controller="root", job_id=job_id ) )
 
     @web.expose
     def data_source_redirect( self, trans, tool_id=None ):
diff --git a/static/maps/mvc/app/app-analysis.js.map b/static/maps/mvc/app/app-analysis.js.map
index 46adcab3f26..dbe3fdf1e53 100644
--- a/static/maps/mvc/app/app-analysis.js.map
+++ b/static/maps/mvc/app/app-analysis.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/static/maps/mvc/app/app-view.js.map b/static/maps/mvc/app/app-view.js.map
index fee8b422b03..8dedaec966a 100644
--- a/static/maps/mvc/app/app-view.js.map
+++ b/static/maps/mvc/app/app-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map
index a7c7c96b5f6..3cd23c051d2 100644
--- a/static/maps/mvc/form/form-input.js.map
+++ b/static/maps/mvc/form/form-input.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/form/form-section.js.map b/static/maps/mvc/form/form-section.js.map
index 5e294c6e43e..e21e3a8f227 100644
--- a/static/maps/mvc/form/form-section.js.map
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diff --git a/static/maps/mvc/form/form-view.js.map b/static/maps/mvc/form/form-view.js.map
index e5a6d5d87a9..09a71c665b7 100644
--- a/static/maps/mvc/form/form-view.js.map
+++ b/static/maps/mvc/form/form-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/tools.js.map b/static/maps/mvc/tools.js.map
index 1da0e0f7ac2..d67e50ab113 100644
--- a/static/maps/mvc/tools.js.map
+++ b/static/maps/mvc/tools.js.map
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diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map
index a49309e9b04..73ee85164ff 100644
--- a/static/maps/mvc/tools/tools-form-base.js.map
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diff --git a/static/maps/mvc/tools/tools-form.js.map b/static/maps/mvc/tools/tools-form.js.map
index 4bd3644e3be..dea05307a24 100644
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diff --git a/static/maps/mvc/ui/ui-misc.js.map b/static/maps/mvc/ui/ui-misc.js.map
index 94760fdae98..3fedba4d03f 100644
--- a/static/maps/mvc/ui/ui-misc.js.map
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diff --git a/static/scripts/mvc/app/app-analysis.js b/static/scripts/mvc/app/app-analysis.js
index 7824ad2b134..9f4036cdb18 100644
--- a/static/scripts/mvc/app/app-analysis.js
+++ b/static/scripts/mvc/app/app-analysis.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools","mvc/upload/upload-view","mvc/ui/ui-misc","mvc/history/options-menu","mvc/history/history-panel-edit-current"],function(a,b,c,d,e,f){var g=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=this.options.params;this.$("#galaxy_main").prop("src",Galaxy.root+(c.tool_id&&"tool_runner?"+$.param(c)||c.workflow_id&&"workflow/run?id="+c.workflow_id||c.m_c&&c.m_c+"/"+c.m_a||Galaxy.config.require_login&&!Galaxy.user.id&&"user/login"||"root/welcome"));var d=this;this.$("#galaxy_main").on("load",function(){$(this).show(),d.$("#center-panel").empty().hide();var a=this.contentWindow;a&&Galaxy.trigger("galaxy_main:load",{fullpath:a.location.pathname+a.location.search+a.location.hash,pathname:a.location.pathname,search:a.location.search,hash:a.location.hash})})},display:function(a){this.$("#galaxy_main").hide(),this.$("#center-panel").empty().scrollTop(0).append(a).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),h=Backbone.View.extend({initialize:function(d){if(this.options=a.merge(d,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var e=new b.ToolSearch({spinner_url:d.spinner_url,search_url:d.search_url,hidden:!1}),f=new b.ToolCollection(d.toolbox),g=new b.ToolPanel({tool_search:e,tools:f,layout:d.toolbox_in_panel});tool_panel_view=new b.ToolPanelView({model:g}),Galaxy.toolPanel=g,g.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var h in d.stored_workflow_menu_entries){var i=d.stored_workflow_menu_entries[h];this.$("#internal-workflows").append(this._templateTool({title:i.stored_workflow.name,href:"workflow/run?id="+i.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new c(d),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),i=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=new d.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}}),g=new d.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"}),h=new d.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});this.components={header:{title:"History",cls:"history-panel-header",buttons:[c,g,h]},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=e(g.$el,{anonymous:!Galaxy.user.id,purgeAllowed:Galaxy.config.allow_user_dataset_purge,root:Galaxy.root}),Galaxy.currHistoryPanel=new f.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:h,center:g,right:i}});
+define(["utils/utils","mvc/tools","mvc/upload/upload-view","mvc/ui/ui-misc","mvc/history/options-menu","mvc/history/history-panel-edit-current","mvc/tools/tools-form"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=this;this.$("#galaxy_main").on("load",function(){var a=this.contentWindow&&this.contentWindow.location;a&&a.host&&($(this).show(),c.$("#center-panel").empty().hide(),Galaxy.trigger("galaxy_main:load",{fullpath:a.pathname+a.search+a.hash,pathname:a.pathname,search:a.search,hash:a.hash}))});var d=$.extend({},Galaxy.params);"upload1"!==d.tool_id&&(d.tool_id||d.job_id)?(d.tool_id&&(d.id=d.tool_id),this.display(new g.View(d).$el)):this.$("#galaxy_main").prop("src",Galaxy.root+(d.workflow_id&&"workflow/run?id="+d.workflow_id||d.m_c&&d.m_c+"/"+d.m_a||Galaxy.config.require_login&&!Galaxy.user.id&&"user/login"||"root/welcome"))},display:function(a){this.$("#galaxy_main").hide(),this.$("#center-panel").empty().scrollTop(0).append(a).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),i=Backbone.View.extend({initialize:function(d){if(this.options=a.merge(d,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var e=new b.ToolSearch({spinner_url:d.spinner_url,search_url:d.search_url,hidden:!1}),f=new b.ToolCollection(d.toolbox),g=new b.ToolPanel({tool_search:e,tools:f,layout:d.toolbox_in_panel});tool_panel_view=new b.ToolPanelView({model:g}),Galaxy.toolPanel=g,g.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var h in d.stored_workflow_menu_entries){var i=d.stored_workflow_menu_entries[h];this.$("#internal-workflows").append(this._templateTool({title:i.stored_workflow.name,href:"workflow/run?id="+i.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new c(d),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),j=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=new d.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}}),g=new d.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"}),h=new d.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});this.components={header:{title:"History",cls:"history-panel-header",buttons:[c,g,h]},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=e(g.$el,{anonymous:!Galaxy.user.id,purgeAllowed:Galaxy.config.allow_user_dataset_purge,root:Galaxy.root}),Galaxy.currHistoryPanel=new f.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:i,center:h,right:j}});
 //# sourceMappingURL=../../../maps/mvc/app/app-analysis.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/app/app-view.js b/static/scripts/mvc/app/app-view.js
index add017f056e..4b36a314e13 100644
--- a/static/scripts/mvc/app/app-view.js
+++ b/static/scripts/mvc/app/app-view.js
@@ -1,2 +1,2 @@
-define(["utils/utils","galaxy.masthead","galaxy.menu","galaxy.frame","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/ui/ui-modal","mvc/user/user-quotameter","mvc/app/app-analysis"],function(a,b,c,d,e,f,g,h,i){return Backbone.View.extend({initialize:function(e){this.options=a.merge(e,{}),this.params=this.options.params,this.setElement(this._template(e)),Galaxy.app=this,$("body").append(this.$el),ensure_dd_helper();var f=$(this.$el.parent()).attr("scroll","no").addClass("full-content");this.options.message_box_visible&&(f.addClass("has-message-box"),this.$("#messagebox").show()),this.options.show_inactivity_warning&&(f.addClass("has-inactivity-box"),this.$("#inactivebox").show()),Galaxy.masthead||(Galaxy.masthead=new b.GalaxyMasthead(e),Galaxy.modal=new g.View,Galaxy.frame=new d.GalaxyFrame,Galaxy.menu=new c.GalaxyMenu({masthead:Galaxy.masthead,config:e}),Galaxy.quotaMeter=new h.UserQuotaMeter({model:Galaxy.user,el:Galaxy.masthead.$(".quota-meter-container")}).render()),this._buildPanels(i,e)},display:function(a,b){$(".select2-hidden-accessible").remove(),this.panels&&this.panels[b||"center"].display(a)},_buildPanels:function(b,c){this.panels=[];var d=["left","center","right"];for(var e in d){var f=d[e],g=this.panels[f]=new b[f](c);if("center"==f)this.$("#center").append(g.$el);else{var h=a.merge(g.components,{header:{title:"",cls:"",buttons:[]},body:{cls:""}}),i=$(this._templatePanel(f));i.find(".panel-header-text").html(h.header.title),i.find(".unified-panel-header-inner").addClass(h.header.cls);for(var e in h.header.buttons)i.find(".panel-header-buttons").append(h.header.buttons[e].$el);i.find(".unified-panel-body").addClass(h.body.cls).append(g.$el);{new Panel({center:this.$("#center"),panel:i,drag:i.find(".unified-panel-footer > .drag"),toggle:i.find(".unified-panel-footer > .panel-collapse"),right:"right"==f})}this.$el.append(i)}}},_templatePanel:function(a){return'<div id="'+a+'"><div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div class="panel-header-buttons" style="float: right"/><div class="panel-header-text"/></div></div><div class="unified-panel-body"/><div class="unified-panel-footer"><div class="panel-collapse '+a+'"/><div class="drag"/></div></div>'},_template:function(){return'<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"><div id="background"/><div id="messagebox" class="panel-'+Galaxy.config.message_box_class+'-message" style="display: none;">'+Galaxy.config.message_box_content+'</div><div id="inactivebox" class="panel-warning-message" style="display: none;">'+Galaxy.config.inactivity_box_content+' <a href="'+Galaxy.root+'user/resend_verification">Resend verification.</a></div><div id="center" class="inbound"/></div>'}})});
+define(["utils/utils","galaxy.masthead","galaxy.menu","galaxy.frame","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/ui/ui-modal","mvc/user/user-quotameter","mvc/app/app-analysis"],function(a,b,c,d,e,f,g,h,i){return Backbone.View.extend({initialize:function(e){this.options=a.merge(e,{}),this.setElement(this._template(e)),Galaxy.app=this,Galaxy.params=this.options.params,Galaxy.router=new Backbone.Router,$("body").append(this.$el),ensure_dd_helper();var f=$(this.$el.parent()).attr("scroll","no").addClass("full-content");this.options.message_box_visible&&(f.addClass("has-message-box"),this.$("#messagebox").show()),this.options.show_inactivity_warning&&(f.addClass("has-inactivity-box"),this.$("#inactivebox").show()),Galaxy.masthead||(Galaxy.masthead=new b.GalaxyMasthead(e),Galaxy.modal=new g.View,Galaxy.frame=new d.GalaxyFrame,Galaxy.menu=new c.GalaxyMenu({masthead:Galaxy.masthead,config:e}),Galaxy.quotaMeter=new h.UserQuotaMeter({model:Galaxy.user,el:Galaxy.masthead.$(".quota-meter-container")}).render()),this._buildPanels(i,e)},display:function(a,b){$(".select2-hidden-accessible").remove(),this.panels&&this.panels[b||"center"].display(a)},_buildPanels:function(b,c){this.panels=[];var d=["left","center","right"];for(var e in d){var f=d[e],g=this.panels[f]=new b[f](c);if("center"==f)this.$("#center").append(g.$el);else{var h=a.merge(g.components,{header:{title:"",cls:"",buttons:[]},body:{cls:""}}),i=$(this._templatePanel(f));i.find(".panel-header-text").html(h.header.title),i.find(".unified-panel-header-inner").addClass(h.header.cls);for(var e in h.header.buttons)i.find(".panel-header-buttons").append(h.header.buttons[e].$el);i.find(".unified-panel-body").addClass(h.body.cls).append(g.$el);{new Panel({center:this.$("#center"),panel:i,drag:i.find(".unified-panel-footer > .drag"),toggle:i.find(".unified-panel-footer > .panel-collapse"),right:"right"==f})}this.$el.append(i)}}},_templatePanel:function(a){return'<div id="'+a+'"><div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div class="panel-header-buttons" style="float: right"/><div class="panel-header-text"/></div></div><div class="unified-panel-body"/><div class="unified-panel-footer"><div class="panel-collapse '+a+'"/><div class="drag"/></div></div>'},_template:function(){return'<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"><div id="background"/><div id="messagebox" class="panel-'+Galaxy.config.message_box_class+'-message" style="display: none;">'+Galaxy.config.message_box_content+'</div><div id="inactivebox" class="panel-warning-message" style="display: none;">'+Galaxy.config.inactivity_box_content+' <a href="'+Galaxy.root+'user/resend_verification">Resend verification.</a></div><div id="center" class="inbound"/></div>'}})});
 //# sourceMappingURL=../../../maps/mvc/app/app-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-input.js b/static/scripts/mvc/form/form-input.js
index 076cd0680fe..ebfb3a7bbaf 100644
--- a/static/scripts/mvc/form/form-input.js
+++ b/static/scripts/mvc/form/form-input.js
@@ -1,2 +1,2 @@
-define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.collapsible?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help,a.argument&&-1==a.help.indexOf("("+a.argument+")")&&(b+=" ("+a.argument+")")),b+="</div>",b+="</div></div>"}})});
+define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element input-name-'+a.name+'"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.collapsible?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help,a.argument&&-1==a.help.indexOf("("+a.argument+")")&&(b+=" ("+a.argument+")")),b+="</div>",b+="</div></div>"}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-section.js b/static/scripts/mvc/form/form-section.js
index ab7900e0827..a4e770695e0 100644
--- a/static/scripts/mvc/form/form-section.js
+++ b/static/scripts/mvc/form/form-section.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,collapsible_value:a.collapsible_value,help:a.help,argument:a.argument,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{name:a.name,label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,collapsible_value:a.collapsible_value,help:a.help,argument:a.argument,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
 //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js
index 9d0e22fa385..c63981f81ab 100644
--- a/static/scripts/mvc/form/form-view.js
+++ b/static/scripts/mvc/form/form-view.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change")}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),$(".tooltip").remove(),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/tools.js b/static/scripts/mvc/tools.js
index a9a630b029e..8b4e4b557da 100644
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -1,2 +1,2 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","mvc/tools/tools-form"],function(a,b,c,d){var e={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},f=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new f(this.toJSON())},set_value:function(a){this.set("value",a||"")}}),g=Backbone.Collection.extend({model:f}),h=f.extend({}),i=f.extend({set_value:function(a){this.set("value",parseInt(a,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),j=i.extend({set_value:function(a){this.set("value",parseFloat(a))}}),k=f.extend({get_samples:function(){return a.map(this.get("options"),function(a){return a[0]})}});f.subModelTypes={integer:i,"float":j,data:h,select:k};var l=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(b){this.set("inputs",new g(a.map(b.inputs,function(a){var b=f.subModelTypes[a.type]||f;return new b(a)})))},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return a.inputs=this.get("inputs").map(function(a){return a.toJSON()}),a},remove_inputs:function(a){var b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new l(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve(new c.DatasetCollection(a))}),f}});a.extend(l.prototype,e);var m=(Backbone.View.extend({}),Backbone.Collection.extend({model:l})),n=Backbone.Model.extend(e),o=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof n?(c=a,c.hide()):a instanceof l&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(o.prototype,e);var p=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:galaxy_config.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length<this.attributes.min_chars_for_search)return void this.set("results",null);var b=a;this.timer&&clearTimeout(this.timer),$("#search-clear-btn").hide(),$("#search-spinner").show();var c=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",galaxy_config.root+"?q="+b),$.get(c.urlRoot,{q:b},function(a){c.set("results",a),$("#search-spinner").hide(),$("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});a.extend(p.prototype,e);{var q=Backbone.Model.extend({initialize:function(a){this.attributes.tool_search=a.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=a.tools,this.attributes.layout=new Backbone.Collection(this.parse(a.layout))},parse:function(b){var c=this,d=function(b){var e=b.model_class;if(e.indexOf("Tool")===e.length-4)return c.attributes.tools.get(b.id);if("ToolSection"===e){var f=a.map(b.elems,d);return b.elems=f,new o(b)}return"ToolSectionLabel"===e?new n(b):void 0};return a.map(b,d)},clear_search_results:function(){this.get("layout").each(function(a){a instanceof o?a.clear_search_results():a.show()})},apply_search_results:function(){var a=this.get("tool_search").get("results");if(null===a)return void this.clear_search_results();var b=null;this.get("layout").each(function(c){c instanceof n?(b=c,b.hide()):c instanceof l?c.apply_search_results(a)&&b&&b.show():(b=null,c.apply_search_results(a))})}}),r=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),s=r.extend({tagName:"div",render:function(){var a=$("<div/>");if(a.append(Handlebars.templates.tool_link(this.model.toJSON())),"upload1"===this.model.id&&a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()}),"Tool"===this.model.get("model_class")){var b=this;a.find("a").on("click",function(a){a.preventDefault();var c=new d.View({id:b.model.id,version:b.model.get("version")});c.deferred.execute(function(){Galaxy.app.display(c.$el)})})}return this.$el.append(a),this}}),t=r.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("<span/>").text(this.model.attributes.text)),this}}),u=r.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){r.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof l){var c=new s({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof n){var d=new t({model:a});d.render(),b.append(d.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),v=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(Handlebars.templates.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new v({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof o){var c=new u({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof l){var d=new s({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof n){var e=new t({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),x=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection}),this.tool_form_view=new x},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:f,IntegerToolParameter:i,SelectToolParameter:k,Tool:l,ToolCollection:m,ToolSearch:p,ToolPanel:q,ToolPanelView:w,ToolFormView:x}});
+define(["libs/underscore","viz/trackster/util","mvc/data","mvc/tools/tools-form"],function(a,b,c,d){var e={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},f=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new f(this.toJSON())},set_value:function(a){this.set("value",a||"")}}),g=Backbone.Collection.extend({model:f}),h=f.extend({}),i=f.extend({set_value:function(a){this.set("value",parseInt(a,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),j=i.extend({set_value:function(a){this.set("value",parseFloat(a))}}),k=f.extend({get_samples:function(){return a.map(this.get("options"),function(a){return a[0]})}});f.subModelTypes={integer:i,"float":j,data:h,select:k};var l=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(b){this.set("inputs",new g(a.map(b.inputs,function(a){var b=f.subModelTypes[a.type]||f;return new b(a)})))},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return a.inputs=this.get("inputs").map(function(a){return a.toJSON()}),a},remove_inputs:function(a){var b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new l(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve(new c.DatasetCollection(a))}),f}});a.extend(l.prototype,e);var m=(Backbone.View.extend({}),Backbone.Collection.extend({model:l})),n=Backbone.Model.extend(e),o=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof n?(c=a,c.hide()):a instanceof l&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(o.prototype,e);var p=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:galaxy_config.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length<this.attributes.min_chars_for_search)return void this.set("results",null);var b=a;this.timer&&clearTimeout(this.timer),$("#search-clear-btn").hide(),$("#search-spinner").show();var c=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",galaxy_config.root+"?q="+b),$.get(c.urlRoot,{q:b},function(a){c.set("results",a),$("#search-spinner").hide(),$("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});a.extend(p.prototype,e);{var q=Backbone.Model.extend({initialize:function(a){this.attributes.tool_search=a.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=a.tools,this.attributes.layout=new Backbone.Collection(this.parse(a.layout))},parse:function(b){var c=this,d=function(b){var e=b.model_class;if(e.indexOf("Tool")===e.length-4)return c.attributes.tools.get(b.id);if("ToolSection"===e){var f=a.map(b.elems,d);return b.elems=f,new o(b)}return"ToolSectionLabel"===e?new n(b):void 0};return a.map(b,d)},clear_search_results:function(){this.get("layout").each(function(a){a instanceof o?a.clear_search_results():a.show()})},apply_search_results:function(){var a=this.get("tool_search").get("results");if(null===a)return void this.clear_search_results();var b=null;this.get("layout").each(function(c){c instanceof n?(b=c,b.hide()):c instanceof l?c.apply_search_results(a)&&b&&b.show():(b=null,c.apply_search_results(a))})}}),r=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),s=r.extend({tagName:"div",render:function(){var a=$("<div/>");if(a.append(Handlebars.templates.tool_link(this.model.toJSON())),"upload1"===this.model.id&&a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()}),"upload1"!==this.model.id&&"Tool"===this.model.get("model_class")){var b=this;a.find("a").on("click",function(a){a.preventDefault();var c=new d.View({id:b.model.id,version:b.model.get("version")});c.deferred.execute(function(){Galaxy.app.display(c.$el)})})}return this.$el.append(a),this}}),t=r.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("<span/>").text(this.model.attributes.text)),this}}),u=r.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){r.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof l){var c=new s({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof n){var d=new t({model:a});d.render(),b.append(d.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),v=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(Handlebars.templates.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new v({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof o){var c=new u({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof l){var d=new s({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof n){var e=new t({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),x=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection}),this.tool_form_view=new x},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:f,IntegerToolParameter:i,SelectToolParameter:k,Tool:l,ToolCollection:m,ToolSearch:p,ToolPanel:q,ToolPanelView:w,ToolFormView:x}});
 //# sourceMappingURL=../../maps/mvc/tools.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js
index da10226a9aa..74faf7889f2 100644
--- a/static/scripts/mvc/tools/tools-form-base.js
+++ b/static/scripts/mvc/tools/tools-form-base.js
@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),Galaxy.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";b.version&&(f+="tool_version="+b.version+"&"),Galaxy.params&&Galaxy.params.tool_id==b.id&&_.each(Galaxy.params,function(a,b){-1==["tool_version","tool_id"].indexOf(b)&&(f+=b+"="+a+"&")})}var g=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!d&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";e.$el.is(":empty")?e.$el.prepend(new c.Message({message:b,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/tools/tools-form.js b/static/scripts/mvc/tools/tools-form.js
index c9793af5045..d7b952222c8 100644
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(a,b,c,d){var e=c.extend({initialize:function(e){var f=this,g=new b.Button({icon:"fa-check",tooltip:"Execute: "+e.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){g.wait(),f.form.portlet.disable(),d.submit(f.form,f.options,function(){g.unwait(),f.form.portlet.enable()})}});e.job_id&&e.job_remap&&(e.inputs.rerun_remap_job_id={label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",e.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."}),e=a.merge(e,{buttons:{execute:g},initial_errors:!0}),c.prototype.initialize.call(this,e)}});return{View:e}});
+define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(a,b,c,d){var e=c.extend({initialize:function(e){var f=this;c.prototype.initialize.call(this,a.merge({customize:function(a){a.buttons={execute:execute_btn=new b.Button({icon:"fa-check",tooltip:"Execute: "+a.name+" ("+a.version+")",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){execute_btn.wait(),f.form.portlet.disable(),d.submit(f.form,a,function(){execute_btn.unwait(),f.form.portlet.enable()})}})},a.job_id&&a.job_remap&&(a.inputs.rerun_remap_job_id={label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",a.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})}},e))}});return{View:e}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-misc.js b/static/scripts/mvc/ui/ui-misc.js
index 40afc4c0eb9..7fe0964ae7b 100644
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-buttons","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{url:"",cls:""}),this.setElement(this._template(this.options))},_template:function(a){return'<img class="ui-image '+a.cls+'" src="'+a.url+'"/>'}}),i=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{title:"",cls:""}),this.setElement(this._template(this.options))},title:function(a){this.$el.html(a)},value:function(){return options.title},_template:function(a){return'<label class="ui-label '+a.cls+'">'+a.title+"</label>"}}),j=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""}),this.setElement(this._template(this.options)),$(this.el).tooltip({title:b.tooltip,placement:"bottom"})},_template:function(a){return'<div><span class="fa '+a.icon+'" class="ui-icon"/>&nbsp;'+a.title+"</div>"}}),k=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{title:"",cls:""}),this.setElement(this._template(this.options)),$(this.el).on("click",b.onclick)},_template:function(a){return'<div><a href="javascript:void(0)" class="ui-anchor '+a.cls+'">'+a.title+"</a></div>"}}),l=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{message:null,status:"info",cls:"",persistent:!1}),this.setElement('<div class="'+this.options.cls+'"/>'),this.options.message&&this.update(this.options)},update:function(b){if(this.options=a.merge(b,this.optionsDefault),""!=b.message){if(this.$el.html(this._template(this.options)),this.$el.find(".alert").append(b.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!b.persistent){var c=this;this.timeout=window.setTimeout(function(){c.$el.is(":visible")?c.$el.fadeOut():c.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(a){return'<div class="ui-message alert alert-'+a.status+'"/>'}}),m=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{onclick:null,searchword:""}),this.setElement(this._template(this.options));var c=this;this.options.onclick&&this.$el.on("submit",function(){var a=c.$el.find("#search");c.options.onclick(a.val())})},_template:function(a){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+a.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}}),n=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1}),this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var c=this;this.$el.on("input",function(){c.options.onchange&&c.options.onchange(c.$el.val())})},value:function(a){return void 0!==a&&this.$el.val(a),this.$el.val()},_template:function(a){return a.area?'<textarea id="'+a.id+'" class="ui-textarea '+a.cls+'"></textarea>':'<input id="'+a.id+'" type="'+a.type+'" value="'+a.value+'" placeholder="'+a.placeholder+'" class="ui-input '+a.cls+'">'}}),o=Backbone.View.extend({initialize:function(a){this.options=a,this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value)},value:function(a){return void 0!==a&&this.$("hidden").val(a),this.$("hidden").val()},_template:function(a){var b='<div id="'+a.id+'" >';return a.info&&(b+="<div>"+a.info+"</div>"),b+='<hidden value="'+a.value+'"/></div>'}});return{Anchor:k,Button:f.ButtonDefault,ButtonIcon:f.ButtonIcon,ButtonCheck:f.ButtonCheck,ButtonMenu:f.ButtonMenu,ButtonLink:f.ButtonLink,Icon:j,Image:h,Input:n,Label:i,Message:l,Modal:g,RadioButton:d.RadioButton,Checkbox:d.Checkbox,Radio:d.Radio,Searchbox:m,Select:b,Hidden:o,Slider:c,Drilldown:e}});
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-buttons","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{url:"",cls:""}),this.setElement(this._template(this.options))},_template:function(a){return'<img class="ui-image '+a.cls+'" src="'+a.url+'"/>'}}),i=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{title:"",cls:""}),this.setElement(this._template(this.options))},title:function(a){this.$el.html(a)},value:function(){return options.title},_template:function(a){return'<label class="ui-label '+a.cls+'">'+a.title+"</label>"}}),j=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""}),this.setElement(this._template(this.options)),$(this.el).tooltip({title:b.tooltip,placement:"bottom"})},_template:function(a){return'<div><span class="fa '+a.icon+'" class="ui-icon"/>&nbsp;'+a.title+"</div>"}}),k=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{title:"",cls:""}),this.setElement(this._template(this.options)),$(this.el).on("click",b.onclick)},_template:function(a){return'<div><a href="javascript:void(0)" class="ui-anchor '+a.cls+'">'+a.title+"</a></div>"}}),l=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{message:null,status:"info",cls:"",persistent:!1}),this.setElement('<div class="'+this.options.cls+'"/>'),this.options.message&&this.update(this.options)},update:function(b){if(this.options=a.merge(b,this.options),""!=b.message){if(this.$el.html(this._template(this.options)),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!b.persistent){var c=this;this.timeout=window.setTimeout(function(){c.$el.is(":visible")?c.$el.fadeOut():c.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(a){var b="ui-message alert alert-"+a.status;return a.large&&(b=("success"==a.status&&"done"||"danger"==a.status&&"error"||a.status)+"messagelarge"),'<div class="'+b+'" >'+a.message+"</div>"}}),m=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{onclick:null,searchword:""}),this.setElement(this._template(this.options));var c=this;this.options.onclick&&this.$el.on("submit",function(){var a=c.$el.find("#search");c.options.onclick(a.val())})},_template:function(a){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+a.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}}),n=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1}),this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var c=this;this.$el.on("input",function(){c.options.onchange&&c.options.onchange(c.$el.val())})},value:function(a){return void 0!==a&&this.$el.val(a),this.$el.val()},_template:function(a){return a.area?'<textarea id="'+a.id+'" class="ui-textarea '+a.cls+'"></textarea>':'<input id="'+a.id+'" type="'+a.type+'" value="'+a.value+'" placeholder="'+a.placeholder+'" class="ui-input '+a.cls+'">'}}),o=Backbone.View.extend({initialize:function(a){this.options=a,this.setElement(this._template(this.options)),void 0!==this.options.value&&this.value(this.options.value)},value:function(a){return void 0!==a&&this.$("hidden").val(a),this.$("hidden").val()},_template:function(a){var b='<div id="'+a.id+'" >';return a.info&&(b+="<div>"+a.info+"</div>"),b+='<hidden value="'+a.value+'"/></div>'}});return{Anchor:k,Button:f.ButtonDefault,ButtonIcon:f.ButtonIcon,ButtonCheck:f.ButtonCheck,ButtonMenu:f.ButtonMenu,ButtonLink:f.ButtonLink,Icon:j,Image:h,Input:n,Label:i,Message:l,Modal:g,RadioButton:d.RadioButton,Checkbox:d.Checkbox,Radio:d.Radio,Searchbox:m,Select:b,Hidden:o,Slider:c,Drilldown:e}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-misc.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
deleted file mode 100644
index 12b6d78e1dd..00000000000
--- a/templates/webapps/galaxy/tool_form.mako
+++ /dev/null
@@ -1,26 +0,0 @@
-<%inherit file="/base.mako"/>
-
-${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
-${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
-
-<%
-    ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
-    ## This avoids making two separate requests since the classic form requires the mako anyway.
-    params = dict(trans.request.params)
-    params['__dataset_id__'] = params.get('id', None)
-    params['__job_id__'] = params.get('job_id', None)
-    self.form_config = tool.to_json(trans, params)
-    self.form_config.update({
-        'id'                : tool.id,
-        'job_id'            : trans.security.encode_id( job.id ) if job else None,
-        'history_id'        : trans.security.encode_id( trans.history.id )
-    })
-%>
-<script>
-    require(['mvc/tools/tools-form'], function(ToolsForm){
-        $(function(){
-            var form = new ToolsForm.View(${ h.dumps(self.form_config) });
-            $('body').append(form.$el);
-        });
-    });
-</script>
\ No newline at end of file
diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py
index cab7989e85b..e7d4ec38778 100644
--- a/test/unit/tools/test_execution.py
+++ b/test/unit/tools/test_execution.py
@@ -399,13 +399,13 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses
         return hdca
 
     def __assert_rerenders_tool_without_errors( self, template, template_vars ):
-        assert template == "tool_form.mako"
+        assert template == ""
         self.__assert_no_errors( template_vars )
         state = template_vars[ "tool_state" ]
         return state
 
     def __assert_exeuted( self, template, template_vars ):
-        if template == "tool_form.mako":
+        if template == "":
             self.__assert_no_errors( template_vars )
         self.assertEquals(
             template,
@@ -414,7 +414,7 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses
         )
 
     def __assert_no_errors( self, template_vars ):
-        assert "errors" in template_vars, "tool_form.mako rendered without errors defintion."
+        assert "errors" in template_vars, "Tool form rendered without error definition."
         errors = template_vars[ "errors" ]
         assert not errors, "Template rendered unexpected errors - %s" % errors