commit/galaxy-central: 3 new changesets

20 Sep 2013

3 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/b8b8a4e16d49/
Changeset:   b8b8a4e16d49
User:        jgoecks
Date:        2013-09-20 19:37:57
Summary:     Modal dialog fixes: (a) scroll when necessary and (b) set maximum height so modal does not overflow viewing window.
Affected #:  6 files

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/scripts/galaxy.panels.js

--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -168,16 +168,17 @@
             this.$overlay.show();
             this.$dialog.show();
             this.$overlay.addClass("in");
-            // Fix min-width so that modal cannot shrink considerably if 
-            // new content is loaded.
+            // Fix min-width so that modal cannot shrink considerably if new content is loaded.
             this.$body.css( "min-width", this.$body.width() );
-            // Set max-height so that modal does not exceed window size.
-            // FIXME: this could perhaps be handled better using a container for the modal 
-            // header-body-footer and setting max-height for the container.
+            // Set max-height so that modal does not exceed window size and is in middle of page.
+            // TODO: this could perhaps be handled better using CSS.
             this.$body.css( "max-height", 
-                            // 2* to provide buffer between bottom of modal and bottom of page.
-                            $(window).height() - 2 * this.$dialog.offset().top - 
-                            this.$footer.outerHeight() - this.$header.outerHeight());
+                            $(window).height() - 
+                            this.$footer.outerHeight() - 
+                            this.$header.outerHeight() -
+                            parseInt( this.$dialog.css( "padding-top" ), 10 ) - 
+                            parseInt( this.$dialog.css( "padding-bottom" ), 10 ) 
+                            );
         }
         // Callback on init
         if ( callback ) {

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -756,6 +756,7 @@
 .btn.active,.btn:active{color:inherit}
 .dropdown-menu{max-width:auto}
 input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex}
+.modal-body{overflow:auto}
 .nav-tabs{margin-bottom:15px}
 a{text-decoration:underline}
 label{font-weight:normal}

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-fugue.png
Binary file static/style/blue/sprite-fugue.png has changed

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-history-buttons.png
Binary file static/style/blue/sprite-history-buttons.png has changed

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-history-states.png
Binary file static/style/blue/sprite-history-states.png has changed

diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/src/less/galaxy_bootstrap/overrides.less
--- a/static/style/src/less/galaxy_bootstrap/overrides.less
+++ b/static/style/src/less/galaxy_bootstrap/overrides.less
@@ -32,6 +32,9 @@
 // Modal -- wider by default, scroll like Trello
 
 /*
+
+NOTE: these styles do not currently work.
+
 .modal { 
   position: absolute;
   top: 50px;
@@ -54,6 +57,11 @@
 }
 */
 
+// Scroll modal body.
+.modal-body {
+  overflow: auto;
+}
+
 // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here
 
 .nav-tabs {


https://bitbucket.org/galaxy/galaxy-central/commits/23abd7b603c8/
Changeset:   23abd7b603c8
User:        jgoecks
Date:        2013-09-20 20:01:49
Summary:     Popup menu implementation: (a) use trigger rather than reimplementing anchor functionality and (b) set URLs for menu options for clarity and utility.
Affected #:  1 file

diff -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -66,7 +66,10 @@
 };
 
 /**
- *  Sets up popupmenu rendering and binds options functions to the appropriate links
+ * Sets up popupmenu rendering and binds options functions to the appropriate links.
+ * initial_options is a dict with text describing the option pointing to either (a) a 
+ * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the 
+ * function to perform. (b) is useful for exposing the underlying URL of the option.
  */
 function make_popupmenu(button_element, initial_options) {
     /*  Use the $.data feature to store options with the link element.
@@ -92,7 +95,9 @@
             }
             $.each( options, function( k, v ) {
                 if (v) {
-                    menu_element.append( $("<li></li>").append( $("<a href='#'></a>").html(k).click(v) ) );
+                    // Action can be either an anonymous function and a mapped dict.
+                    var action = v.action || v;
+                    menu_element.append( $("<li></li>").append( $("<a>").attr("href", v.url).html(k).click(action) ) );
                 } else {
                     menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) );
                 }
@@ -164,43 +169,24 @@
                 options[ link.text() ] = null;
                 
             } else {
-                options[ link.text() ] = function() {
+                options[ link.text() ] = {
+                    url: href,
+                    action: function() {
 
-                    // if theres confirm text, send the dialog
-                    if ( !confirmtext || confirm( confirmtext ) ) {
-                        var f;
-                        // relocate the center panel
-                        if ( target === "_parent" ) {
-                            window.parent.location = href;
-                            
-                        // relocate the entire window
-                        } else if ( target === "_top" ) {
-                            window.top.location = href;
-                            
-                        // Http request target is a window named demolocal on the local box
-                        } else if ( target === "demo" ) {
-                            if ( f === undefined || f.closed ) {
-                                f = window.open( href,target );
-                                f.creator = self;
+                        // if theres confirm text, send the dialog
+                        if ( !confirmtext || confirm( confirmtext ) ) {
+                            var f;    
+                            // Http request target is a window named demolocal on the local box
+                             if ( target === "demo" ) {
+                                if ( f === undefined || f.closed ) {
+                                    f = window.open( href,target );
+                                    f.creator = self;
+                                }
+                                
                             }
-                            
-                        // this panel or other, valid panels
-                        } else {
-                            // it may be that the button and menu href are not in the same frame:
-                            //  allow certain frame names to be used as a target
-                            var other_valid_targets = [
-                                'galaxy_main'
-                                // following are blocked until needed
-                                //'galaxy_tools',
-                                //'galaxy_history'
-                            ];
-                            if( ( target && ( target in window )
-                            &&  ( other_valid_targets.indexOf( target ) !== -1 ) ) ){
-                                window[ target ].location = href;
-
-                            // relocate this panel
-                            } else {
-                                window.location = href;
+                            // For all other links, do the default action.
+                            else {
+                                link.trigger('click');
                             }
                         }
                     }


https://bitbucket.org/galaxy/galaxy-central/commits/66d484a18d19/
Changeset:   66d484a18d19
User:        jgoecks
Date:        2013-09-21 04:50:51
Summary:     Automated merge.
Affected #:  34 files

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -209,6 +209,7 @@
         if self.nginx_upload_store:
             self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
         self.object_store = kwargs.get( 'object_store', 'disk' )
+        self.object_store_check_old_style = string_as_bool( kwargs.get( 'object_store_check_old_style', False ) )
         self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root )
         # Handle AWS-specific config options for backward compatibility
         if kwargs.get( 'aws_access_key', None) is not None:

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -25,7 +25,7 @@
 from galaxy.datatypes.metadata import MetadataCollection
 from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
 from galaxy.security import get_permitted_actions
-from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail
+from galaxy.util import asbool, is_multi_byte, nice_size, Params, restore_text, send_mail
 from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.web.framework.helpers import to_unicode
@@ -34,6 +34,7 @@
         WorkflowMappingField)
 from sqlalchemy.orm import object_session
 from sqlalchemy.sql.expression import func
+from tool_shed.util import common_util
 
 log = logging.getLogger( __name__ )
 
@@ -3463,7 +3464,28 @@
     @property
     def has_repository_dependencies( self ):
         if self.metadata:
-            return 'repository_dependencies' in self.metadata
+            repository_dependencies_dict = self.metadata.get( 'repository_dependencies', {} )
+            repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+            # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
+            for rd_tup in repository_dependencies:
+                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+                    common_util.parse_repository_dependency_tuple( rd_tup )
+                if not asbool( only_if_compiling_contained_td ):
+                    return True
+        return False
+
+    @property
+    def has_repository_dependencies_only_if_compiling_contained_td( self ):
+        if self.metadata:
+            repository_dependencies_dict = self.metadata.get( 'repository_dependencies', {} )
+            repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+            # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
+            for rd_tup in repository_dependencies:
+                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+                    common_util.parse_repository_dependency_tuple( rd_tup )
+                if not asbool( only_if_compiling_contained_td ):
+                    return False
+            return True
         return False
 
     @property
@@ -3695,10 +3717,14 @@
 
     @property
     def tuples_of_repository_dependencies_needed_for_compiling_td( self ):
-        """Return this repository's repository dependencies that are necessary only for compiling this repository's tool dependencies."""
+        """
+        Return tuples defining this repository's repository dependencies that are necessary only for compiling this repository's tool
+        dependencies.
+        """
         rd_tups_of_repositories_needed_for_compiling_td = []
-        if self.has_repository_dependencies:
-            rd_tups = self.metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
+        if self.metadata:
+            repository_dependencies = self.metadata.get( 'repository_dependencies', None )
+            rd_tups = repository_dependencies[ 'repository_dependencies' ]
             for rd_tup in rd_tups:
                 if len( rd_tup ) == 6: 
                     tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/objectstore/__init__.py
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -198,6 +198,7 @@
         super(DiskObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs)
         self.file_path = file_path or config.file_path
         self.config = config
+        self.check_old_style = config.object_store_check_old_style
         self.extra_dirs['job_work'] = config.job_working_directory
         self.extra_dirs['temp'] = config.new_file_path
         if extra_dirs is not None:
@@ -264,14 +265,13 @@
         return os.path.abspath(path)
 
     def exists(self, obj, **kwargs):
-        path = self._construct_path(obj, old_style=True, **kwargs)
-        # For backward compatibility, check root path first; otherwise, construct
-        # and check hashed path
-        if os.path.exists(path):
-            return True
-        else:
-            path = self._construct_path(obj, **kwargs)
-            return os.path.exists(path)
+        if self.check_old_style:
+            path = self._construct_path(obj, old_style=True, **kwargs)
+            # For backward compatibility, check root path first; otherwise, construct
+            # and check hashed path
+            if os.path.exists(path):
+                return True
+        return os.path.exists(self._construct_path(obj, **kwargs))
 
     def create(self, obj, **kwargs):
         if not self.exists(obj, **kwargs):
@@ -320,13 +320,13 @@
         return content
 
     def get_filename(self, obj, **kwargs):
-        path = self._construct_path(obj, old_style=True, **kwargs)
-        # For backward compatibility, check root path first; otherwise, construct
-        # and return hashed path
-        if os.path.exists(path):
-            return path
-        else:
-            return self._construct_path(obj, **kwargs)
+        if self.check_old_style:
+            path = self._construct_path(obj, old_style=True, **kwargs)
+            # For backward compatibility, check root path first; otherwise, construct
+            # and return hashed path
+            if os.path.exists(path):
+                return path
+        return self._construct_path(obj, **kwargs)
 
     def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """ `create` parameter is not used in this implementation """

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -587,8 +587,10 @@
         hda_dict[ 'api_type' ] = "file"
 
         # Add additional attributes that depend on trans can hence must be added here rather than at the model level.
-
-        #NOTE: access is an expensive operation - removing it and adding the precondition of access is already checked
+        can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+        can_access_hda = ( trans.user_is_admin() or can_access_hda )
+        if not can_access_hda:
+            return self.get_inaccessible_hda_dict( trans, hda )
         hda_dict[ 'accessible' ] = True
 
         # ---- return here if deleted AND purged OR can't access
@@ -634,6 +636,18 @@
 
         return trans.security.encode_dict_ids( hda_dict )
 
+    def get_inaccessible_hda_dict( self, trans, hda ):
+        return trans.security.encode_dict_ids({
+            'id'        : hda.id,
+            'history_id': hda.history.id,
+            'hid'       : hda.hid,
+            'name'      : hda.name,
+            'state'     : hda.state,
+            'deleted'   : hda.deleted,
+            'visible'   : hda.visible,
+            'accessible': False
+        })
+
     def get_hda_dict_with_error( self, trans, hda, error_msg='' ):
         return trans.security.encode_dict_ids({
             'id'        : hda.id,

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -198,7 +198,10 @@
             if page_num == 0:
                 # Show all rows in page.
                 total_num_rows = query.count()
+                # persistant page='all'
                 page_num = 1
+                #page_num = 'all'
+                #extra_url_args['page'] = page_num
                 num_pages = 1
             else:
                 # Show a limited number of rows. Before modifying query, get the total number of rows that query

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -235,8 +235,15 @@
             # get file destination
             file_destination = dataset.get_file_name()
 
+            # check if the directory exists
+            dn = os.path.dirname(file_destination)
+            if not os.path.exists(dn):
+                os.makedirs(dn)
+    
+            # get file and directory names
+            fn = os.path.basename(content.filename)
+    
             # save file locally
-            fn = os.path.basename(content.filename)
             open(file_destination, 'wb').write(content.file.read())
             
             # log

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -812,7 +812,7 @@
         status = kwd.get( 'status', 'done' )
         shed_tool_conf = kwd.get( 'shed_tool_conf', None )
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        # Handle repository dependencies.
+        # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies.
         has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) )
         install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' )
         # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
@@ -1061,7 +1061,7 @@
                                                                               repository_clone_url,
                                                                               metadata,
                                                                               trans.model.ToolShedRepository.installation_status.NEW,
-                                                                              tool_shed_repository.installed_changeset_revision,
+                                                                              tool_shed_repository.changeset_revision,
                                                                               tool_shed_repository.owner,
                                                                               tool_shed_repository.dist_to_shed )
         ctx_rev = suc.get_ctx_rev( trans.app,
@@ -1320,7 +1320,6 @@
         missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
         repository_name = dependencies_for_repository_dict.get( 'name', None )
         repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
-
         if installed_repository_dependencies or missing_repository_dependencies:
             has_repository_dependencies = True
         else:

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -309,7 +309,6 @@
                 # If deleting the current history, make a new current.
                 if history == trans.get_history():
                     deleted_current = True
-                    trans.get_or_create_default_history()
                 trans.log_event( "History (%s) marked as deleted" % history.name )
                 n_deleted += 1
             if purge and trans.app.config.allow_user_dataset_purge:
@@ -339,6 +338,8 @@
                 part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance"
             message_parts.append( "%s.  " % part )
         if deleted_current:
+            #note: this needs to come after commits above or will use an empty history that was deleted above
+            trans.get_or_create_default_history()
             message_parts.append( "Your active history was deleted, a new empty history is now active.  " )
             status = INFO
         return ( status, " ".join( message_parts ) )

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -73,6 +73,7 @@
             "changeset_revision": "3a08cc21466f",
             "downloadable": true,
             "has_repository_dependencies": false,
+            "has_repository_dependencies_only_if_compiling_contained_td": false,
             "id": "f9cad7b01a472135",
             "includes_datatypes": false,
             "includes_tool_dependencies": false,
@@ -125,7 +126,8 @@
                                                                  action='show',
                                                                  id=encoded_repository_metadata_id )
                 # Get the repo_info_dict for installing the repository.
-                repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies = \
+                repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
+                    has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
                     repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision )
                 return repository_dict, repository_metadata_dict, repo_info_dict
             else:

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1343,32 +1343,36 @@
     def get_changeset_revision_and_ctx_rev( self, trans, **kwd ):
         """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
         def has_galaxy_utilities( repository_metadata ):
-            includes_data_managers = False
-            includes_datatypes = False
-            includes_tools = False
-            includes_tools_for_display_in_tool_panel = False
-            has_repository_dependencies = False
-            includes_tool_dependencies = False
-            includes_workflows = False
+            has_galaxy_utilities_dict = dict( includes_data_managers=False,
+                                              includes_datatypes=False,
+                                              includes_tools=False,
+                                              includes_tools_for_display_in_tool_panel=False,
+                                              has_repository_dependencies=False,
+                                              has_repository_dependencies_only_if_compiling_contained_td=False,
+                                              includes_tool_dependencies=False,
+                                              includes_workflows=False )
             if repository_metadata:
                 includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
                 metadata = repository_metadata.metadata
                 if metadata:
                     if 'data_manager' in metadata:
-                        includes_data_managers = True
+                        has_galaxy_utilities_dict[ 'includes_data_managers' ] = True
                     if 'datatypes' in metadata:
-                        includes_datatypes = True
+                        has_galaxy_utilities_dict[ 'includes_datatypes' ] = True
                     if 'tools' in metadata:
-                        includes_tools = True
+                        has_galaxy_utilities_dict[ 'includes_tools' ] = True
                     if 'tool_dependencies' in metadata:
-                        includes_tool_dependencies = True
-                    if 'repository_dependencies' in metadata:
-                        has_repository_dependencies = True
+                        has_galaxy_utilities_dict[ 'includes_tool_dependencies' ] = True
+                    repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
+                    repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+                    has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
+                        suc.get_repository_dependency_types( repository_dependencies )
+                    has_galaxy_utilities_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
+                    has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = \
+                        has_repository_dependencies_only_if_compiling_contained_td
                     if 'workflows' in metadata:
-                        includes_workflows = True
-            return includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
+                        has_galaxy_utilities_dict[ 'includes_workflows' ] = True
+            return has_galaxy_utilities_dict
         name = kwd.get( 'name', None )
         owner = kwd.get( 'owner', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
@@ -1376,8 +1380,15 @@
         repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
                                                                                  trans.security.encode_id( repository.id ),
                                                                                  changeset_revision )
-        includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \
-            has_galaxy_utilities( repository_metadata )
+        has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata )
+        includes_data_managers = has_galaxy_utilities_dict[ 'includes_data_managers' ]
+        includes_datatypes = has_galaxy_utilities_dict[ 'includes_datatypes' ]
+        includes_tools = has_galaxy_utilities_dict[ 'includes_tools' ]
+        includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict[ 'includes_tools_for_display_in_tool_panel' ]
+        includes_tool_dependencies = has_galaxy_utilities_dict[ 'includes_tool_dependencies' ]
+        has_repository_dependencies = has_galaxy_utilities_dict[ 'has_repository_dependencies' ]
+        has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ]
+        includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ]
         repo_dir = repository.repo_path( trans.app )
         repo = hg.repository( suc.get_configured_ui(), repo_dir )
         # Default to the received changeset revision and ctx_rev.
@@ -1392,6 +1403,7 @@
                             includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
                             includes_tool_dependencies=includes_tool_dependencies,
                             has_repository_dependencies=has_repository_dependencies,
+                            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
                             includes_workflows=includes_workflows )
         if changeset_revision == repository.tip( trans.app ):
             # If changeset_revision is the repository tip, there are no additional updates.
@@ -1407,6 +1419,7 @@
                 for changeset in repo.changelog:
                     includes_tools = False
                     has_repository_dependencies = False
+                    has_repository_dependencies_only_if_compiling_contained_td = False
                     changeset_hash = str( repo.changectx( changeset ) )
                     ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                     if update_to_changeset_hash:
@@ -1414,8 +1427,15 @@
                                                                                                            trans.security.encode_id( repository.id ),
                                                                                                            changeset_hash )
                         if update_to_repository_metadata:
-                            includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \
-                                has_galaxy_utilities( update_to_repository_metadata )
+                            has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata )
+                            includes_data_managers = has_galaxy_utilities_dict[ 'includes_data_managers' ]
+                            includes_datatypes = has_galaxy_utilities_dict[ 'includes_datatypes' ]
+                            includes_tools = has_galaxy_utilities_dict[ 'includes_tools' ]
+                            includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict[ 'includes_tools_for_display_in_tool_panel' ]
+                            includes_tool_dependencies = has_galaxy_utilities_dict[ 'includes_tool_dependencies' ]
+                            has_repository_dependencies = has_galaxy_utilities_dict[ 'has_repository_dependencies' ]
+                            has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ]
+                            includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ]
                             # We found a RepositoryMetadata record.
                             if changeset_hash == repository.tip( trans.app ):
                                 # The current ctx is the repository tip, so use it.
@@ -1435,6 +1455,7 @@
                 update_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies
                 update_dict[ 'includes_workflows' ] = includes_workflows
                 update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
+                update_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td
                 update_dict[ 'changeset_revision' ] = str( latest_changeset_revision )
         update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() )
         return encoding_util.tool_shed_encode( update_dict )
@@ -1611,14 +1632,18 @@
         includes_tools = False
         includes_tools_for_display_in_tool_panel = False
         has_repository_dependencies = False
+        has_repository_dependencies_only_if_compiling_contained_td = False
         includes_tool_dependencies = False
         repo_info_dicts = []
         for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
             repository_id, changeset_revision = tup
-            repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, cur_has_repository_dependencies = \
+            repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \
+                cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \
                 repository_util.get_repo_info_dict( trans, repository_id, changeset_revision )
             if cur_has_repository_dependencies and not has_repository_dependencies:
                 has_repository_dependencies = True
+            if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
+                has_repository_dependencies_only_if_compiling_contained_td = True
             if cur_includes_tools and not includes_tools:
                 includes_tools = True
             if cur_includes_tool_dependencies and not includes_tool_dependencies:
@@ -1629,6 +1654,7 @@
         return dict( includes_tools=includes_tools,
                      includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
                      has_repository_dependencies=has_repository_dependencies,
+                     has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
                      includes_tool_dependencies=includes_tool_dependencies,
                      repo_info_dicts=repo_info_dicts )
 
@@ -1708,7 +1734,9 @@
         tool_version_dicts = []
         for changeset in repo.changelog:
             current_changeset_revision = str( repo.changectx( changeset ) )
-            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+                                                                                     trans.security.encode_id( repository.id ),
+                                                                                     current_changeset_revision )
             if repository_metadata and repository_metadata.tool_versions:
                 tool_version_dicts.append( repository_metadata.tool_versions )
                 if current_changeset_revision == changeset_revision:
@@ -1766,22 +1794,30 @@
                 includes_workflows = True
             readme_files_dict = readme_util.build_readme_files_dict( metadata )
         # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies.
+        has_repository_dependencies = False
+        has_repository_dependencies_only_if_compiling_contained_td = False
+        includes_tool_dependencies = False
         for name, repo_info_tuple in repo_info_dict.items():
-            description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
-                suc.get_repo_info_tuple_contents( repo_info_tuple )
-            if repository_dependencies:
-                has_repository_dependencies = True
-            else:
-                has_repository_dependencies = False
-            if tool_dependencies:
-                includes_tool_dependencies = True
-            else:
-                includes_tool_dependencies = False
+            if not has_repository_dependencies or not has_repository_dependencies_only_if_compiling_contained_td or not includes_tool_dependencies:
+                description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
+                    suc.get_repo_info_tuple_contents( repo_info_tuple )
+                for rd_key, rd_tups in repository_dependencies.items():
+                    if rd_key in [ 'root_key', 'description' ]:
+                        continue
+                    curr_has_repository_dependencies, curr_has_repository_dependencies_only_if_compiling_contained_td = \
+                        suc.get_repository_dependency_types( rd_tups )
+                    if curr_has_repository_dependencies and not has_repository_dependencies:
+                        has_repository_dependencies = True
+                    if curr_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
+                        has_repository_dependencies_only_if_compiling_contained_td = True
+                if tool_dependencies and not includes_tool_dependencies:
+                    includes_tool_dependencies = True
         return dict( includes_data_managers=includes_data_managers,
                      includes_datatypes=includes_datatypes,
                      includes_tools=includes_tools,
                      includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
                      has_repository_dependencies=has_repository_dependencies,
+                     has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
                      includes_tool_dependencies=includes_tool_dependencies,
                      includes_workflows=includes_workflows,
                      readme_files_dict=readme_files_dict,
@@ -2434,7 +2470,9 @@
                     try:
                         commands.remove( repo.ui, repo, selected_file, force=True )
                     except Exception, e:
-                        log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e ))
+                        log.debug( "Error removing the following file using the mercurial API:\n %s" % str( selected_file ) )
+                        log.debug( "The error was: %s" % str( e ))
+                        log.debug( "Attempting to remove the file using a different approach." )
                         relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' )
                         repo.dirstate.remove( relative_selected_file )
                         repo.dirstate.write()

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/tool_shed/model/__init__.py
--- a/lib/galaxy/webapps/tool_shed/model/__init__.py
+++ b/lib/galaxy/webapps/tool_shed/model/__init__.py
@@ -253,6 +253,7 @@
         self.time_last_tested = time_last_tested
         self.tool_test_results = tool_test_results
         self.has_repository_dependencies = has_repository_dependencies
+        # We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here.
         self.includes_datatypes = includes_datatypes
         self.includes_tools = includes_tools
         self.includes_tool_dependencies = includes_tool_dependencies

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -234,10 +234,10 @@
         else:
             includes_tools = False
         includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
-        if 'repository_dependencies' in metadata:
-            has_repository_dependencies = True
-        else:
-            has_repository_dependencies = False
+        repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
+        repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
+            suc.get_repository_dependency_types( repository_dependencies )
         if 'tool_dependencies' in metadata:
             includes_tool_dependencies = True
         else:
@@ -246,6 +246,7 @@
         # Here's where we may have to handle enhancements to the callers. See above comment.
         includes_tools = False
         has_repository_dependencies = False
+        has_repository_dependencies_only_if_compiling_contained_td = False
         includes_tool_dependencies = False
         includes_tools_for_display_in_tool_panel = False
     ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
@@ -259,7 +260,8 @@
                                             repository_metadata=repository_metadata,
                                             tool_dependencies=None,
                                             repository_dependencies=None )
-    return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies
+    return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
+        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
 
 def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys ):
     """
@@ -311,6 +313,7 @@
             includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False )
             includes_workflows = update_dict.get( 'includes_workflows', False )
             has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False )
+            has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
             changeset_revision = update_dict.get( 'changeset_revision', None )
             ctx_rev = update_dict.get( 'ctx_rev', None )
         changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers
@@ -320,6 +323,7 @@
         changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies
         changeset_revision_dict[ 'includes_workflows' ] = includes_workflows
         changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
+        changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td
         changeset_revision_dict[ 'changeset_revision' ] = changeset_revision
         changeset_revision_dict[ 'ctx_rev' ] = ctx_rev
     except Exception, e:
@@ -331,6 +335,7 @@
         changeset_revision_dict[ 'includes_tool_dependencies' ] = False
         changeset_revision_dict[ 'includes_workflows' ] = False
         changeset_revision_dict[ 'has_repository_dependencies' ] = False
+        changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False
         changeset_revision_dict[ 'changeset_revision' ] = None
         changeset_revision_dict[ 'ctx_rev' ] = None
     return changeset_revision_dict

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -394,7 +394,7 @@
                                         if not binary_installed:
                                             print 'Binary installation did not occur, so proceeding with install and compile recipe.'
                                             # Make sure to reset for installation if attempt at binary installation resulted in an error.
-                                            if tool_dependency.status != app.model.ToolDependency.installation_status.NEW:
+                                            if tool_dependency.status != app.model.ToolDependency.installation_status.NEVER_INSTALLED:
                                                 removed, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency )
                                             install_via_fabric( app, 
                                                                 tool_dependency, 

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -12,6 +12,7 @@
 from tool_shed.util import encoding_util
 from tool_shed.util import data_manager_util
 from tool_shed.util import datatype_util
+from tool_shed.util import tool_dependency_util
 from tool_shed.util import tool_util
 from tool_shed.util import xml_util
 from tool_shed.galaxy_install.tool_dependencies.install_util import install_package
@@ -69,16 +70,28 @@
     Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined
     by the received repo_info_dict.
     """
+    repository = None
+    installed_rd = {}
+    installed_td = {}
+    missing_rd = {}
+    missing_td = {}
     name = repo_info_dict.keys()[ 0 ]
     repo_info_tuple = repo_info_dict[ name ]
-    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
+    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
         suc.get_repo_info_tuple_contents( repo_info_tuple )
+    if tool_dependencies:
+        if not includes_tool_dependencies:
+            includes_tool_dependencies = True
+        # Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies.  We don't add to installed_td
+        # and missing_td here because at this point they are empty.
+        installed_td, missing_td = get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies )
+    # In cases where a repository dependency is required only for compiling a dependent repository's tool dependency, the value of
+    # repository_dependencies will be an empty dictionary here.
     if repository_dependencies:
         # We have a repository with one or more defined repository dependencies.
         missing_td = {}
-        # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the re-installation process.
-        # In this case, a record for the repository will exist in the database with the status of 'New'.
-        repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
+        if not repository:
+            repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
         if repository and repository.metadata:
             installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
         else:
@@ -86,73 +99,70 @@
         # Discover all repository dependencies and retrieve information for installing them.
         all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
         has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
+        has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
         includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
         includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
         includes_tools = all_repo_info_dict.get( 'includes_tools', False )
         required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
         # Display tool dependencies defined for each of the repository dependencies.
         if required_repo_info_dicts:
-            all_tool_dependencies = {}
+            required_tool_dependencies = {}
             for rid in required_repo_info_dicts:
                 for name, repo_info_tuple in rid.items():
-                    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, rid_installed_td = \
+                    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
                         suc.get_repo_info_tuple_contents( repo_info_tuple )
-                    if rid_installed_td:
-                        for td_key, td_dict in rid_installed_td.items():
-                            if td_key not in all_tool_dependencies:
-                                all_tool_dependencies[ td_key ] = td_dict
-            if all_tool_dependencies:
-                if installed_td is None:
-                    installed_td = {}
-                else:
-                    # Move all tool dependencies to the missing_tool_dependencies container.
-                    for td_key, td_dict in installed_td.items():
-                        if td_key not in missing_td:
-                            missing_td[ td_key ] = td_dict
-                    installed_td = {}
+                    if rid_tool_dependencies:
+                        for td_key, td_dict in rid_tool_dependencies.items():
+                            if td_key not in required_tool_dependencies:
+                                required_tool_dependencies[ td_key ] = td_dict
+            if required_tool_dependencies:
                 # Discover and categorize all tool dependencies defined for this repository's repository dependencies.
-                required_tool_dependencies, required_missing_tool_dependencies = \
-                    get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies )
-                if required_tool_dependencies:
+                required_installed_td, required_missing_td = get_installed_and_missing_tool_dependencies( trans,
+                                                                                                          tool_shed_url,
+                                                                                                          required_tool_dependencies )
+                if required_installed_td:
                     if not includes_tool_dependencies:
                         includes_tool_dependencies = True
-                    for td_key, td_dict in required_tool_dependencies.items():
+                    for td_key, td_dict in required_installed_td.items():
                         if td_key not in installed_td:
                             installed_td[ td_key ] = td_dict
-                if required_missing_tool_dependencies:
+                if required_missing_td:
                     if not includes_tool_dependencies:
                         includes_tool_dependencies = True
-                    for td_key, td_dict in required_missing_tool_dependencies.items():
+                    for td_key, td_dict in required_missing_td.items():
                         if td_key not in missing_td:
                             missing_td[ td_key ] = td_dict
     else:
-        # We have a single repository with no defined repository dependencies.
+        # We have a single repository with (possibly) no defined repository dependencies.
         all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
         has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
+        has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
         includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
         includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
         includes_tools = all_repo_info_dict.get( 'includes_tools', False )
         required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
-        installed_rd = None
-        missing_rd = None
-        missing_td = None
-    dependencies_for_repository_dict = dict( changeset_revision=changeset_revision,
-                                             has_repository_dependencies=has_repository_dependencies,
-                                             includes_tool_dependencies=includes_tool_dependencies,
-                                             includes_tools=includes_tools,
-                                             includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                                             installed_repository_dependencies=installed_rd,
-                                             installed_tool_dependencies=installed_td,
-                                             missing_repository_dependencies=missing_rd,
-                                             missing_tool_dependencies=missing_td,
-                                             name=name,
-                                             repository_owner=repository_owner )
+    dependencies_for_repository_dict = \
+        dict( changeset_revision=changeset_revision,
+              has_repository_dependencies=has_repository_dependencies,
+              has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
+              includes_tool_dependencies=includes_tool_dependencies,
+              includes_tools=includes_tools,
+              includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+              installed_repository_dependencies=installed_rd,
+              installed_tool_dependencies=installed_td,
+              missing_repository_dependencies=missing_rd,
+              missing_tool_dependencies=missing_td,
+              name=name,
+              repository_owner=repository_owner )
     return dependencies_for_repository_dict
 
 def get_installed_and_missing_repository_dependencies( trans, repository ):
     """
     Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but
-    may or may not be installed.  In this case, the repository dependencies are associated with the repository in the database.
+    may or may not be installed.  In this case, the repository dependencies are associated with the repository in the database.  Do not
+    include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these
+    special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if
+    that tool dependency requires compilation.
     """
     missing_repository_dependencies = {}
     installed_repository_dependencies = {}
@@ -166,7 +176,14 @@
         for tsr in repository.repository_dependencies:
             prior_installation_required = suc.set_prior_installation_required( repository, tsr )
             only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr )
-            rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, tsr.changeset_revision, prior_installation_required, only_if_compiling_contained_td, tsr.id, tsr.status ]
+            rd_tup = [ tsr.tool_shed,
+                       tsr.name,
+                       tsr.owner,
+                       tsr.changeset_revision,
+                       prior_installation_required,
+                       only_if_compiling_contained_td,
+                       tsr.id,
+                       tsr.status ]
             if tsr.status == trans.model.ToolShedRepository.installation_status.INSTALLED:
                 installed_rd_tups.append( rd_tup )
             else:
@@ -184,7 +201,7 @@
             repository_dependencies = metadata.get( 'repository_dependencies', {} )
             description = repository_dependencies.get( 'description', None )
             # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the missing_repository_dependencies
-            # dictionary for proper display parsing.
+            # dictionaries for proper display parsing.
             root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed,
                                                                                            repository.name,
                                                                                            repository.owner,
@@ -210,7 +227,7 @@
     installed_repository_dependencies = {}
     missing_rd_tups = []
     installed_rd_tups = []
-    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
+    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
         suc.get_repo_info_tuple_contents( repo_info_tuple )
     if repository_dependencies:
         description = repository_dependencies[ 'description' ]
@@ -228,7 +245,7 @@
                 # tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td )
                 tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup )
                 tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
-                repository, current_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple )
+                repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple )
                 if repository:
                     new_rd_tup = [ tool_shed,
                                   name,
@@ -273,29 +290,46 @@
         missing_repository_dependencies[ 'description' ] = description
     return installed_repository_dependencies, missing_repository_dependencies
 
-def get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ):
+def get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies_dict ):
     """Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy."""
-    # FIXME: confirm that this method currently populates and returns only missing tool dependencies.  If so, this method should be enhanced to search for
-    # installed tool dependencies defined as complex repository dependency relationships.
-    if all_tool_dependencies:
-        tool_dependencies = {}
-        missing_tool_dependencies = {}
-        for td_key, val in all_tool_dependencies.items():
-            # Set environment tool dependencies are a list, set each member to never installed.
+    installed_tool_dependencies = {}
+    missing_tool_dependencies = {}
+    if tool_dependencies_dict:
+        for td_key, val in tool_dependencies_dict.items():
+            # Default the status to NEVER_INSTALLED.
+            tool_dependency_status = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
+            # Set environment tool dependencies are a list.
             if td_key == 'set_environment':
                 new_val = []
                 for requirement_dict in val:
-                    requirement_dict[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
+                    # {'repository_name': 'xx', 'name': 'bwa', 'version': '0.5.9', 'repository_owner': 'yy', 'changeset_revision': 'zz', 'type': 'package'}
+                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type( trans.app,
+                                                                                                     requirement_dict.get( 'name', None ),
+                                                                                                     requirement_dict.get( 'version', None ),
+                                                                                                     requirement_dict.get( 'type', 'package' ) )
+                    if tool_dependency:
+                        tool_dependency_status = tool_dependency.status
+                    requirement_dict[ 'status' ] = tool_dependency_status
                     new_val.append( requirement_dict )
-                missing_tool_dependencies[ td_key ] = new_val
+                    if tool_dependency_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]:
+                        installed_tool_dependencies[ td_key ] = new_val
+                    else:
+                        missing_tool_dependencies[ td_key ] = new_val
             else:
-                # Since we have a new install, missing tool dependencies have never been installed.
-                val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED
+                # The val dictionary looks something like this:
+                # {'repository_name': 'xx', 'name': 'bwa', 'version': '0.5.9', 'repository_owner': 'yy', 'changeset_revision': 'zz', 'type': 'package'}
+                tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type( trans.app,
+                                                                                                 val.get( 'name', None ),
+                                                                                                 val.get( 'version', None ),
+                                                                                                 val.get( 'type', 'package' ) )
+                if tool_dependency:
+                    tool_dependency_status = tool_dependency.status
+                val[ 'status' ] = tool_dependency_status
+            if tool_dependency_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]:
+                installed_tool_dependencies[ td_key ] = val
+            else:
                 missing_tool_dependencies[ td_key ] = val
-    else:
-        tool_dependencies = None
-        missing_tool_dependencies = None
-    return tool_dependencies, missing_tool_dependencies
+    return installed_tool_dependencies, missing_tool_dependencies
 
 def get_required_repo_info_dicts( trans, tool_shed_url, repo_info_dicts ):
     """
@@ -328,7 +362,9 @@
                             toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key )
                             components_list = [ toolshed, name, owner, changeset_revision ]
                             only_if_compiling_contained_td = 'False'
-                        # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository.
+                        # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since
+                        # in this case, the repository dependency is really a dependency of the dependent repository's contained tool dependency, and only if
+                        # that tool dependency requires compilation.
                         if not util.asbool( only_if_compiling_contained_td ):
                             if components_list not in required_repository_tups:
                                 required_repository_tups.append( components_list )
@@ -337,8 +373,8 @@
                                 only_if_compiling_contained_td = components_list[ 5 ]
                             except:
                                 only_if_compiling_contained_td = 'False'
-                            # TODO: Fix this to display the tool dependency if only_if_compiling_contained_td is True, but clarify that installation may not
-                            # happen.
+                            # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository
+                            # (see above comment).
                             if not util.asbool( only_if_compiling_contained_td ):
                                 if components_list not in required_repository_tups:
                                     required_repository_tups.append( components_list )

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -1,3 +1,4 @@
+import logging
 import os
 import urllib2
 from galaxy.util import json
@@ -5,6 +6,8 @@
 from tool_shed.util import encoding_util
 from tool_shed.util import xml_util
 
+log = logging.getLogger( __name__ )
+
 REPOSITORY_OWNER = 'devteam'
 
 def accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies ):

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -280,13 +280,16 @@
 def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ):
     """Create or update a repository_metadatqa record in the tool shed."""
     has_repository_dependencies = False
+    has_repository_dependencies_only_if_compiling_contained_td = False
     includes_datatypes = False
     includes_tools = False
     includes_tool_dependencies = False
     includes_workflows = False
     if metadata_dict:
-        if 'repository_dependencies' in metadata_dict:
-            has_repository_dependencies = True
+        repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} )
+        repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
+            suc.get_repository_dependency_types( repository_dependencies )
         if 'datatypes' in metadata_dict:
             includes_datatypes = True
         if 'tools' in metadata_dict:
@@ -295,7 +298,11 @@
             includes_tool_dependencies = True
         if 'workflows' in metadata_dict:
             includes_workflows = True
-    downloadable = has_repository_dependencies or includes_datatypes or includes_tools or includes_tool_dependencies or includes_workflows
+    if has_repository_dependencies or has_repository_dependencies_only_if_compiling_contained_td or includes_datatypes or \
+        includes_tools or includes_tool_dependencies or includes_workflows:
+        downloadable = True
+    else:
+        downloadable = False
     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
     if repository_metadata:
         # A repository metadata record already exists with the received changeset_revision, so we don't need to check the skip_tool_test table.
@@ -1851,10 +1858,13 @@
                     repository_metadata.includes_datatypes = True
                 else:
                     repository_metadata.includes_datatypes = False
-                if 'repository_dependencies' in metadata_dict:
-                    repository_metadata.has_repository_dependencies = True
-                else:
-                    repository_metadata.has_repository_dependencies = False
+                # We don't store information about the special type of repository dependency that is needed only for compiling a tool dependency
+                # defined for the dependent repository.
+                repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} )
+                repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
+                has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
+                    suc.get_repository_dependency_types( repository_dependencies )
+                repository_metadata.has_repository_dependencies = has_repository_dependencies
                 if 'tool_dependencies' in metadata_dict:
                     repository_metadata.includes_tool_dependencies = True
                 else:

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/repository_dependency_util.py
--- a/lib/tool_shed/util/repository_dependency_util.py
+++ b/lib/tool_shed/util/repository_dependency_util.py
@@ -139,6 +139,7 @@
                     # repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed.
                     if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies:
                         if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR,
+                                                                      trans.model.ToolShedRepository.installation_status.NEW,
                                                                       trans.model.ToolShedRepository.installation_status.UNINSTALLED ]:
                             # The current tool shed repository is not currently installed, so we can update it's record in the database.
                             can_update = True

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -868,6 +868,31 @@
                          .first()
     return None
 
+def get_repository_dependency_types( repository_dependencies ):
+    """
+    Inspect the received list of repository_dependencies tuples and return boolean values for has_repository_dependencies and
+    has_repository_dependencies_only_if_compiling_contained_td.
+    """
+    # Set has_repository_dependencies, which will be True only if at least one repository_dependency is defined with the value of
+    # only_if_compiling_contained_td as False.
+    has_repository_dependencies = False
+    for rd_tup in repository_dependencies:
+        tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+            common_util.parse_repository_dependency_tuple( rd_tup )
+        if not asbool( only_if_compiling_contained_td ):
+            has_repository_dependencies = True
+            break
+    # Set has_repository_dependencies_only_if_compiling_contained_td, which will be True only if at least one repository_dependency is
+    # defined with the value of only_if_compiling_contained_td as True.
+    has_repository_dependencies_only_if_compiling_contained_td = False
+    for rd_tup in repository_dependencies:
+        tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+            common_util.parse_repository_dependency_tuple( rd_tup )
+        if asbool( only_if_compiling_contained_td ):
+            has_repository_dependencies_only_if_compiling_contained_td = True
+            break
+    return has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
+
 def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ):
     """Return an installed tool_shed_repository database record that is defined by either the current changeset revision or the installed_changeset_revision."""
     # This method is used only in Galaxy, not the tool shed.
@@ -1389,14 +1414,23 @@
 
 def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ):
     """
-    Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated
-    in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one
-    that was previously installed.  We'll look in the database instead of on disk since the repository may be uninstalled.
+    Find out if a repository is already installed into Galaxy - there are several scenarios where this is necessary.  For example, this method
+    will handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated
+    in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one that was
+    previously installed.  We'll look in the database instead of on disk since the repository may be currently uninstalled.
     """
     description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
         get_repo_info_tuple_contents( repo_info_tuple )
     tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
-    # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset
+    # See if we can locate the repository using the value of changeset_revision.
+    tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app,
+                                                                                                     tool_shed,
+                                                                                                     repository_name,
+                                                                                                     repository_owner,
+                                                                                                     changeset_revision )
+    if tool_shed_repository:
+        return tool_shed_repository, changeset_revision
+    # Get all previous changeset revisions from the tool shed for the repository back to, but excluding, the previous valid changeset
     # revision to see if it was previously installed using one of them.
     url = url_join( tool_shed_url,
                     'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
@@ -1410,14 +1444,14 @@
                                                                                                              repository_name,
                                                                                                              repository_owner,
                                                                                                              previous_changeset_revision )
-            if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]:
+            if tool_shed_repository:
                 return tool_shed_repository, previous_changeset_revision
     return None, None
 
 def reset_previously_installed_repository( trans, repository ):
     """
     Reset the atrributes of a tool_shed_repository that was previsouly installed.  The repository will be in some state other than with a
-    status of INSTALLED, so all atributes will be set to the default (NEW( state.  This will enable the repository to be freshly installed.
+    status of INSTALLED, so all atributes will be set to the default NEW state.  This will enable the repository to be freshly installed.
     """
     repository.deleted = False
     repository.tool_shed_status = None

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/tool_dependency_util.py
--- a/lib/tool_shed/util/tool_dependency_util.py
+++ b/lib/tool_shed/util/tool_dependency_util.py
@@ -258,6 +258,14 @@
                                     app.model.ToolDependency.table.c.type == type ) ) \
                      .first()
 
+def get_tool_dependency_by_name_version_type( app, name, version, type ):
+    sa_session = app.model.context.current
+    return sa_session.query( app.model.ToolDependency ) \
+                     .filter( and_( app.model.ToolDependency.table.c.name == name,
+                                    app.model.ToolDependency.table.c.version == version,
+                                    app.model.ToolDependency.table.c.type == type ) ) \
+                     .first()
+
 def get_tool_dependency_by_name_version_type_repository( app, repository, name, version, type ):
     sa_session = app.model.context.current
     return sa_session.query( app.model.ToolDependency ) \

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/tool_util.py
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
@@ -962,7 +962,7 @@
         suc.config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path )
 
 def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ):
-    """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly."""
+    """A tool shed repository is being deactivated or uninstalled, so handle tool panel alterations accordingly."""
     # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed
     # in the same way when the repository is activated or reinstalled.
     tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository )

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.grids.js
--- a/static/scripts/galaxy.grids.js
+++ b/static/scripts/galaxy.grids.js
@@ -472,7 +472,7 @@
         go_to_URL();
         return;
     }
-    
+
     // If there's an operation, do POST; otherwise, do GET.
     var method = (grid.get('operation') ? "POST" : "GET" );
     $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions.
@@ -565,4 +565,4 @@
     
     // return
     return true;
-}
\ No newline at end of file
+}

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.modal.js
--- a/static/scripts/galaxy.modal.js
+++ b/static/scripts/galaxy.modal.js
@@ -77,13 +77,25 @@
             // link functions
             $.each(options.buttons, function(name, value)
             {
-                 footer.append($('<button></button>').text(name).click(value)).append(" ");
+                 footer.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" ");
             });
         } else
             // default close button
             footer.append($('<button></button>').text('Close').click(function() { self.hide() })).append(" ");
     },
     
+    // enable buttons
+    enable: function(name)
+    {
+        $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', false);
+    },
+
+    // disable buttons
+    disable: function(name)
+    {
+        $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true);
+    },
+        
     /*
         HTML TEMPLATES
     */

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.upload.js
--- a/static/scripts/galaxy.upload.js
+++ b/static/scripts/galaxy.upload.js
@@ -1,5 +1,5 @@
 /*
-    galaxy upload v1.0
+    galaxy upload
 */
 
 // dependencies
@@ -14,12 +14,20 @@
     // button
     button_show : null,
     
-    // file counter
-    file_counter: 0,
+    // upload mod
+    uploadbox: null,
     
     // initialize
     initialize : function()
     {
+        // wait for galaxy history panel (workaround due to the use of iframes)
+        if (!Galaxy.currHistoryPanel)
+        {
+            var self = this;
+            window.setTimeout(function() { self.initialize() }, 500)
+            return;
+        }
+        
         // add activate icon
         var self = this;
         this.button_show = new mod_master.GalaxyMasterIcon (
@@ -37,87 +45,252 @@
     // events
     events :
     {
-        'mouseover'      : 'event_mouseover',
-        'mouseleave'     : 'event_mouseleave'
+        'mouseover'         : 'event_mouseover',
+        'mouseleave'        : 'event_mouseleave'
     },
     
     // mouse over
     event_mouseover : function (e)
     {
-        $('#galaxy-upload-box').addClass('highlight');
     },
     
     // mouse left
     event_mouseleave : function (e)
     {
-        $('#galaxy-upload-box').removeClass('highlight');
     },
 
     // start
-    event_start : function(index, file, message)
+    event_announce : function(index, file, message)
     {
+        // hide info
+        this.uploadbox.info().hide();
+        
         // make id
-        var id = '#galaxy-upload-file-' + index;
+        var id = '#upload-' + index;
         
-        // add tag
-        $('#galaxy-upload-box').append(this.template_file(id));
+        // add upload item
+        $(this.el).append(this.template_file(id));
+        
+        // scroll to bottom
+        $(this.el).scrollTop($(this.el).prop('scrollHeight'));
+        
+        // access upload item
+        var it = this.get_upload_item(index);
+        
+        // fade in
+        it.fadeIn();
         
         // update title
-        $('#galaxy-upload-file-' + index).find('.title').html(file.name);
+        it.find('.title').html(file.name);
         
+        // configure select field
+        it.find('#extension').select2(
+        {
+            placeholder: 'Auto-detect',
+            width: 'copy',
+            ajax: {
+                url: "http://www.weighttraining.com/sm/search",
+                dataType: 'jsonp',
+                quietMillis: 100,
+                data: function(term, page)
+                {
+                    return {
+                        types: ["exercise"],
+                        limit: -1,
+                        term: term
+                    };
+                },
+                results: function(data, page)
+                {
+                    return { results: data.results.exercise }
+                }
+            },
+            formatResult: function(exercise)
+            {
+                return "<div class='select2-user-result'>" + exercise.term + "</div>";
+            },
+            formatSelection: function(exercise)
+            {
+                return exercise.term;
+            },
+            initSelection : function (element, callback)
+            {
+                var elementText = $(element).attr('data-init-text');
+                callback({"term":elementText});
+            }
+        });
+        
+        // add functionality to remove button
+        var self = this;
+        it.find('.remove').on('click', function() { self.event_remove (index) });
+    
         // initialize progress
         this.event_progress(index, file, 0);
         
-        // update counter
-        this.file_counter++;
-        this.refresh();
+        // update button status
+        this.modal.enable('Upload');
+        this.modal.enable('Reset');
+    },
+    
+    // start
+    event_initialize : function(index, file, message)
+    {
+        // update on screen counter
+        this.button_show.number(message);
+    
+        // get element
+        var it = this.get_upload_item(index);
+        
+        // read in configuration
+        var data = {
+            source          : "upload",
+            space_to_tabs   : it.find('#space_to_tabs').is(':checked'),
+            extension       : it.find('#extension').val()
+        }
+        
+        // return additional data to be send with file
+        return data;
     },
     
     // progress
     event_progress : function(index, file, message)
     {
-        // get progress bar
-        var el = $('#galaxy-upload-file-' + index);
+        // get element
+        var it = this.get_upload_item(index);
         
         // get value
         var percentage = parseInt(message);
         
         // update progress
-        el.find('.progress').css({ width : percentage + '%' });
+        it.find('.progress-bar').css({ width : percentage + '%' });
         
         // update info
-        el.find('.info').html(percentage + '% of ' + this.size_to_string (file.size));
+        it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size));
     },
     
     // end
     event_success : function(index, file, message)
-    {
+    {        
+        // get element
+        var it = this.get_upload_item(index);
+        
+        // update progress frame
+        it.addClass('panel-success');
+        it.removeClass('panel-default');
+        
         // update galaxy history
         Galaxy.currHistoryPanel.refresh();
         
-        // update counter
-        this.file_counter--;
-        this.refresh();
+        // make sure progress is shown correctly
+        this.event_progress(index, file, 100);
+        
+        // update on screen counter
+        this.button_show.number('');
     },
     
     // end
     event_error : function(index, file, message)
     {
-        // get file box
-        var el = $('#galaxy-upload-file-' + index);
+        // get element
+        var it = this.get_upload_item(index);
         
         // update progress frame
-        el.find('.progress-frame').addClass('failed');
+        it.addClass('panel-danger');
+        it.removeClass('panel-default');
         
-        // update error message
-        el.find('.error').html("<strong>Failed:</strong> " + message);
-
-        // update progress
+        // remove progress bar
+        it.find('.progress').remove();
+        
+        // write error message
+        it.find('.error').html('<strong>Failed:</strong> ' + message);
+        
+        // make sure progress is shown correctly
         this.event_progress(index, file, 0);
         
-        // update counter
-        this.file_counter--;
-        this.refresh();
+        // update on screen counter
+        this.button_show.number('');
+    },
+    
+    // start upload process
+    event_upload : function()
+    {
+        // hide configuration
+        $(this.el).find('.panel-body').hide();
+        
+        // switch icon
+        $(this.el).find('.remove').each(function()
+        {
+            $(this).removeClass('fa-icon-trash');
+            $(this).addClass('fa-icon-caret-down');
+        });
+        
+        // update button status
+        this.modal.disable('Upload');
+        
+        // configure url
+        var current_history = Galaxy.currHistoryPanel.model.get('id');
+        this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"});
+        
+        // initiate upload procedure in plugin
+        this.uploadbox.upload();
+    },
+    
+    // remove all
+    event_reset : function()
+    {
+        // remove from screen
+        var panels = $(this.el).find('.panel');
+        var self = this;
+        panels.fadeOut({complete: function()
+        {
+            // remove panels
+            panels.remove();
+                    
+            // show on screen info
+            self.uploadbox.info().fadeIn();
+        }});
+        
+        // update button status
+        this.modal.disable('Upload');
+        this.modal.disable('Reset');
+        
+        // remove from queue
+        this.uploadbox.reset();
+    },
+    
+    // remove item from upload list
+    event_remove : function(index)
+    {
+        // remove
+        var self = this;
+        var it = this.get_upload_item(index);
+        
+        // fade out and update button status
+        it.fadeOut({complete: function()
+        {
+            // remove from screen
+            it.remove();
+        
+            // remove from queue
+            self.uploadbox.remove(index);
+        
+            // update reset button
+            if ($(self.el).find('.panel').length > 0)
+                self.modal.enable('Reset');
+            else {
+                // disable reset button
+                self.modal.disable('Reset');
+                
+                // show on screen info
+                self.uploadbox.info().fadeIn();
+            }
+            
+            // update upload button
+            if (self.uploadbox.length() > 0)
+                self.modal.enable('Upload');
+            else
+                self.modal.disable('Upload');
+        }});
     },
     
     // show/hide upload frame
@@ -126,14 +299,6 @@
         // prevent default
         e.preventDefault();
         
-        // wait for galaxy history panel (workaround due to the use of iframes)
-        if (!Galaxy.currHistoryPanel)
-        {
-            var self = this;
-            window.setTimeout(function() { self.event_show(e) }, 200)
-            return;
-        }
-        
         // create modal
         if (!this.modal)
         {
@@ -142,44 +307,45 @@
             this.modal = new mod_modal.GalaxyModal(
             {
                 title   : 'Upload files from your local drive',
-                body    : this.template(),
+                body    : this.template('upload-box'),
                 buttons : {
-                    'Close' : function() {self.modal.hide()}
+                    'Select' : function() {self.uploadbox.select()},
+                    'Upload' : function() {self.event_upload()},
+                    'Reset'  : function() {self.event_reset()},
+                    'Close'  : function() {self.modal.hide()}
                 }
             });
         
-            // get current history
-            var current_history = Galaxy.currHistoryPanel.model.get('id');
-        
+            // set element
+            this.setElement('#upload-box');
+            
             // file upload
             var self = this;
-            $('#galaxy-upload-box').uploadbox(
+            this.uploadbox = this.$el.uploadbox(
             {
-                url             : galaxy_config.root + "api/histories/" + current_history + "/contents",
                 dragover        : self.event_mouseover,
                 dragleave       : self.event_mouseleave,
-                start           : function(index, file, message) { self.event_start(index, file, message) },
+                announce        : function(index, file, message) { self.event_announce(index, file, message) },
+                initialize      : function(index, file, message) { return self.event_initialize(index, file, message) },
                 success         : function(index, file, message) { self.event_success(index, file, message) },
                 progress        : function(index, file, message) { self.event_progress(index, file, message) },
                 error           : function(index, file, message) { self.event_error(index, file, message) },
-                data            : {source : "upload"}
             });
             
-            // set element
-            this.setElement('#galaxy-upload-box');
+            // update button status
+            this.modal.disable('Upload');
+            this.modal.disable('Reset');
         }
-        
+                
         // show modal
         this.modal.show();
     },
 
-    // update counter
-    refresh: function ()
+    // get upload item
+    get_upload_item: function(index)
     {
-        if (this.file_counter > 0)
-            this.button_show.number(this.file_counter);
-        else
-            this.button_show.number('');
+        // get element
+        return $(this.el).find('#upload-' + index);
     },
 
     // to string
@@ -197,21 +363,32 @@
     },
 
     // load html template
-    template: function()
+    template: function(id)
     {
-        return  '<form id="galaxy-upload-box" class="galaxy-upload-box"></form>';
+        return  '<div id="' + id + '" class="upload-box"></div>';
     },
     
     // load html template
     template_file: function(id)
     {
-        return  '<div id="' + id.substr(1) + '" class="file corner-soft shadow">' +
-                    '<div class="title"></div>' +
-                    '<div class="error"></div>' +
-                    '<div class="progress-frame corner-soft">' +
-                        '<div class="progress"></div>' +
+        return  '<div id="' + id.substr(1) + '" class="panel panel-default">' +
+                    '<div class="panel-heading">' +
+                        '<h5 class="title"></h5>' +
+                        '<h5 class="info"></h5>' +
+                        '<div class="remove fa-icon-trash"></div>' +
                     '</div>' +
-                    '<div class="info"></div>' +
+                    '<div class="panel-body">' +
+                        '<div class="menu">' +
+                            //'<input id="extension" type="hidden" width="10px"/> ' +
+                            '<span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span>' +
+                        '</div>' +
+                    '</div>' +
+                    '<div class="panel-footer">' +
+                        '<div class="progress">' +
+                            '<div class="progress-bar progress-bar-success"></div>' +
+                        '</div>' +
+                        '<h6 class="error"></h6>' +
+                    '</div>' +
                 '</div>';
     }
 });

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/packed/galaxy.upload.js
--- a/static/scripts/packed/galaxy.upload.js
+++ b/static/scripts/packed/galaxy.upload.js
@@ -1,1 +1,1 @@
-define(["utils/galaxy.css","galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(c,b,d){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){c.load_file("static/style/galaxy.upload.css");var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){$("#galaxy-upload-box").addClass("galaxy-upload-highlight")},event_mouseleave:function(f){$("#galaxy-upload-box").removeClass("galaxy-upload-highlight")},event_start:function(e,f,g){var h="#galaxy-upload-file-"+e;$("#galaxy-upload-box").append(this.template_file(h));$("#galaxy-upload-file-"+e).find(".title").html(f.name);this.event_progress(e,f,0);this.file_counter++;this.refresh()},event_progress:function(f,g,i){var h=$("#galaxy-upload-file-"+f);var e=parseInt(i);h.find(".progress").css({width:e+"%"});h.find(".info").html(e+"% of "+this.size_to_string(g.size))},event_success:function(e,f,g){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(e,f,h){var g=$("#galaxy-upload-file-"+e);g.find(".progress-frame").addClass("failed");g.find(".error").html("<strong>Failed:</strong> "+h);this.event_progress(e,f,0);this.file_counter--;this.refresh()},event_show:function(h){h.preventDefault();if(!Galaxy.currHistoryPanel){var g=this;window.setTimeout(function(){g.event_show(h)},200);return}if(!this.modal){this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template()});var f=Galaxy.currHistoryPanel.model.get("id");var g=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+f+"/contents",dragover:g.event_mouseover,dragleave:g.event_mouseleave,start:function(e,i,j){g.event_start(e,i,j)},success:function(e,i,j){g.event_success(e,i,j)},progress:function(e,i,j){g.event_progress(e,i,j)},error:function(e,i,j){g.event_error(e,i,j)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box galaxy-corner"></form>'},template_file:function(e){return'<div id="'+e.substr(1)+'" class="galaxy-upload-file galaxy-corner-soft galaxy-shadow"><div class="title"></div><div class="error"></div><div class="progress-frame galaxy-corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}});
\ No newline at end of file
+define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){$("#galaxy-upload-box").addClass("highlight")},event_mouseleave:function(d){$("#galaxy-upload-box").removeClass("highlight")},event_start:function(d,e,f){var g="#galaxy-upload-file-"+d;$("#galaxy-upload-box").append(this.template_file(g));$("#galaxy-upload-file-"+d).find(".title").html(e.name);this.event_progress(d,e,0);this.file_counter++;this.refresh()},event_progress:function(e,f,h){var g=$("#galaxy-upload-file-"+e);var d=parseInt(h);g.find(".progress").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,f){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(d,e,g){var f=$("#galaxy-upload-file-"+d);f.find(".progress-frame").addClass("failed");f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.file_counter--;this.refresh()},event_show:function(g){g.preventDefault();if(!Galaxy.currHistoryPanel){var f=this;window.setTimeout(function(){f.event_show(g)},200);return}if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template(),buttons:{Close:function(){f.modal.hide()}}});var d=Galaxy.currHistoryPanel.model.get("id");var f=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+d+"/contents",dragover:f.event_mouseover,dragleave:f.event_mouseleave,start:function(e,h,i){f.event_start(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box"></form>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="file corner-soft shadow"><div class="title"></div><div class="error"></div><div class="progress-frame corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}});
\ No newline at end of file

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/packed/galaxy.workflow_editor.canvas.js
--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js
@@ -1,1 +1,1 @@
-function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output.  All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
+function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa-icon-remove").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output.  All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa-icon-remove").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/utils/galaxy.uploadbox.js
--- a/static/scripts/utils/galaxy.uploadbox.js
+++ b/static/scripts/utils/galaxy.uploadbox.js
@@ -1,5 +1,5 @@
 /*
-    galaxy upload lib v1.0 - uses FileReader, FormData and XMLHttpRequest
+    galaxy upload lib - uses FileReader, FormData and XMLHttpRequest
 */
 ;(function($)
 {
@@ -11,67 +11,71 @@
     {
         url             : '',
         paramname       : 'content',
-        maxfilesize     : 2048,
-        data            : {},
+        maxfilesize     : 250,
         dragover        : function() {},
         dragleave       : function() {},
+        announce        : function() {},
         initialize      : function() {},
-        start           : function() {},
         progress        : function() {},
         success         : function() {},
         error           : function(index, file, message) { alert(message); },
         error_browser   : "Your browser does not support drag-and-drop file uploads.",
-        error_filesize  : "This file is too large. Please use an FTP client to upload it.",
-        error_default   : "The upload failed. Please make sure the file is available and accessible.",
-        text_default    : "Drag&drop files here or click to browse your local drive.",
-        text_degrade    : "Click here to browse your local drive. <br><br>Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."
+        error_filesize  : "This file is too large (>250MB). Please use an FTP client to upload it.",
+        error_default   : "Please make sure the file is available.",
+        text_default    : "Drag&drop files into this box or click 'Select' to select files!",
+        text_degrade    : "Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."
     }
 
-    // global file queue
-    var queue = [];
+    // options
+    var opts = {};
+
+    // file queue
+    var queue = {};
   
-    // global counter for file being currently processed
-    var queue_index = -1;
+    // counter for file being currently processed
+    var queue_index = 0;
   
-    // global queue status
+    // queue length
+    var queue_length = 0;
+  
+    // indicates if queue is currently running
     var queue_status = false;
   
+    // element
+    var el = null;
+  
     // attach to element
     $.fn.uploadbox = function(options)
     {
         // parse options
-        var opts = $.extend({}, default_opts, options);
+        opts = $.extend({}, default_opts, options);
   
         // compatibility
         var mode = window.File && window.FileReader && window.FormData && window.XMLHttpRequest;
   
+        // element
+        el = this;
+  
         // append upload button
-        this.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');
-        this.append('<div id="uploadbox_info"></div>');
+        el.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');
+        el.append('<div id="uploadbox_info"></div>');
   
         // set info text
         if (mode)
-            this.find('#uploadbox_info').html(opts.text_default);
+            el.find('#uploadbox_info').html(opts.text_default);
         else
-            this.find('#uploadbox_info').html(opts.text_degrade);
+            el.find('#uploadbox_info').html(opts.text_degrade);
   
         // attach events
-        this.on('drop', drop);
-        this.on('dragover',  dragover);
-        this.on('dragleave', dragleave);
-  
-        // attach click event
-        this.on('click', function(e)
-        {
-            e.stopPropagation();
-            $('#uploadbox_input').trigger(e);
-        });
+        el.on('drop', drop);
+        el.on('dragover',  dragover);
+        el.on('dragleave', dragleave);
   
         // attach change event
         $('#uploadbox_input').change(function(e)
         {
-            var files = e.target.files;
-            upload(files);
+            // add files to queue
+            add(e.target.files);
         });
 
         // drop event
@@ -81,11 +85,8 @@
             if(!e.dataTransfer)
                 return;
             
-            // get files from event
-            var files = e.dataTransfer.files;
-  
-            // start upload
-            upload(files);
+            // add files to queue
+            add(e.dataTransfer.files);
       
             // prevent default
             e.preventDefault();
@@ -98,14 +99,14 @@
         function dragover(e)
         {
             e.preventDefault();
-            opts.dragover.call(this, e);
+            opts.dragover.call(e);
         }
 
         // drag leave
         function dragleave(e)
         {
             e.stopPropagation();
-            opts.dragleave.call(this, e);
+            opts.dragleave.call(e);
         }
 
         // progress
@@ -117,39 +118,61 @@
         }
 
         // respond to an upload request
-        function upload(files)
+        function add(files)
         {
-            // get current queue size
-            var queue_sofar = queue.length;
+            // add new files to queue
+            for (var i = 0; i < files.length; i++)
+            {
+                // new identifier
+                var index = String(++queue_index);
   
-            // add new files to queue
-            for (var index = 0; index < files.length; index++)
-                queue.push(files[index]);
+                // add to queue
+                queue[index] = files[i];
   
-            // tell client about new uploads
-            for (var index = queue_sofar; index < queue.length; index++)
-                opts.start(index, queue[index], "");
+                // increase counter
+                queue_length++;
   
-            // initiate processing loop if process loop is not running already
-            if (!queue_status)
-                process();
+                // announce
+                opts.announce(index, queue[index], "");
+            }
         }
 
+        // remove entry from queue
+        function remove(index)
+        {
+            if (queue[index])
+            {
+                // remove from queue
+                delete queue[index];
+  
+                // update counter
+                queue_length--;
+            }
+        }
+  
         // process an upload, recursive
         function process()
         {
-            // check if for files
-            if (queue_index + 1 == queue.length)
+            // get an identifier from the queue
+            var index = -1;
+            for (var key in queue)
             {
-                queue_status = false;
-                return;
+                index = key;
+                break;
             }
   
-            // set status
-            queue_status = true;
+            // validate
+            if (queue_length == 0)
+                return;
   
-            // identify current index
-            var index = ++queue_index;
+            // get current file from queue
+            var file = queue[index];
+  
+            // remove from queue
+            remove(index)
+  
+            // start
+            var data = opts.initialize(index, file, length);
   
             // add file to queue
             try
@@ -158,50 +181,45 @@
                 var reader = new FileReader();
   
                 // identify maximum file size
-                var file = queue[index];
                 var filesize = file.size;
                 var maxfilesize = 1048576 * opts.maxfilesize;
-                    
+    
                 // set index
                 reader.index = index;
                 if (filesize < maxfilesize)
                 {
-                    // link loadend is always called at the end
-                    reader.onloadend = function(e)
+                    // link load
+                    reader.onload = function(e)
                     {
-                        send(index, file)
+                        send(index, file, data)
                     };
 
                     // link error
                     reader.onerror = function(e)
                     {
-                        opts.error(index, file, opts.error_default);
-                        queue_status = false;
+                        error(index, file, opts.error_default);
                     };
 
                     // read data
                     reader.readAsDataURL(file);
                 } else {
                     // skip file
-                    opts.error(index, file, opts.error_filesize);
-  
-                    // restart process
-                    process();
+                    error(index, file, opts.error_filesize);
                 }
             } catch (err)
             {
                 // parse error
-                opts.error(index, file, err);
+                error(index, file, err);
             }
         }
   
         // send file
-        function send (index, file)
+        function send (index, file, data)
         {
             // construct form data
             var formData = new FormData();
-            for (var key in opts.data)
-                formData.append(key, opts.data[key]);
+            for (var key in data)
+                formData.append(key, data[key]);
             formData.append(opts.paramname, file, file.name);
   
             // prepare request
@@ -237,22 +255,94 @@
                 // pass any error to the error option
                 if (xhr.status < 200 || xhr.status > 299)
                 {
+                    // format error
+                    var text = xhr.statusText;
+                    if (!xhr.statusText)
+                        text = opts.error_default;
+  
                     // request error
-                    opts.error(index, file, xhr.statusText + " (Server Code " + xhr.status + ")");
-  
-                    // reset status
-                    queue_status = false;
-                } else {
+                    error(index, file, text + " (Server Code " + xhr.status + ")");
+                } else
                     // parse response
-                    opts.success(index, file, response);
-
-                    // upload next file
-                    process();
-                }
+                    success(index, file, response);
             }
         }
   
-        // return
-        return this;
+        // success
+        function success (index, file, msg)
+        {
+            // parse message
+            opts.success(index, file, msg);
+  
+            // restart process after success
+            process();
+        }
+  
+        // error
+        function error (index, file, err)
+        {
+            // parse error
+            opts.error(index, file, err);
+  
+            // restart process after error
+            process();
+        }
+  
+        /*
+            public interface
+        */
+    
+        // open file browser for selection
+        function select()
+        {
+            $('#uploadbox_input').trigger('click');
+        }
+  
+        // remove all entries from queue
+        function reset(index)
+        {
+            for (index in queue)
+                remove(index);
+        }
+  
+        // initiate upload process
+        function upload()
+        {
+            if (!queue_status)
+                process();
+        }
+  
+        // current queue length
+        function length()
+        {
+            return queue_length;
+        }
+  
+        // set options
+        function configure(options)
+        {
+            // update current configuration
+            opts = $.extend({}, opts, options);
+  
+            // return new configuration
+            return opts;
+        }
+  
+        // visibility of on screen information
+        function info()
+        {
+            return el.find('#uploadbox_info');
+        }
+  
+        // export functions
+        return {
+            'select'    : select,
+            'remove'    : remove,
+            'upload'    : upload,
+            'reset'     : reset,
+            'length'    : length,
+            'configure' : configure,
+            'info'      : info
+        };
     }
 })(jQuery);
\ No newline at end of file

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1123,15 +1123,12 @@
 .galaxy-frame .frame .f-close{right:5px;top:1px}
 .galaxy-frame .frame .f-pin{left:6px;top:1px}
 .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px}
-.galaxy-upload-box{width:100%;height:200px;max-height:200px;padding:10px 0px 0px 0px;text-align:center;cursor:pointer;overflow:scroll;font-size:12px;line-height:1.428571429;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf}.galaxy-upload-box .corner-soft{-moz-border-radius:3px;border-radius:3px}
-.galaxy-upload-box .shadow{-webkit-box-shadow:0 0 2px rgba(0,0,0,0.3)}
-.galaxy-upload-box .highlight{border:1px dashed #333}
-.galaxy-upload-box .file{position:relative;margin:5px 20px 5px 20px;border:1px solid #bfbfbf;color:#333}.galaxy-upload-box .file .title{margin:3px 130px 0px 5px;text-align:left;overflow:hidden;border:0px}
-.galaxy-upload-box .file .progress-frame{border:0px;margin:0px 5px 3px 5px;height:7px;background:#bfbfbf}
-.galaxy-upload-box .file .progress{background:#5cb85c;height:100%;width:0%}
-.galaxy-upload-box .file .failed{background:#d9534f}
-.galaxy-upload-box .file .error{font-size:11px;text-align:left;overflow:hidden;margin:0px 5px 0px 5px}
-.galaxy-upload-box .file .info{position:absolute;top:4px;right:5px;font-size:11px;text-align:right;overflow:hidden;max-width:100px;max-height:12px}
+.upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden}
+.upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px}
+.upload-box .panel .panel-heading .remove{position:absolute;cursor:pointer;top:0px;right:3px}
+.upload-box .panel .panel-body{position:relative;padding:5px}
+.upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px}
+.upload-box .panel .panel-footer .error{font-weight:normal;margin:2px}
 .unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}
 .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%}
 .clear:before,.clear:after{content:" ";display:table;}
@@ -1392,9 +1389,9 @@
 div.historyItem-setting_metadata{background:#ffc}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif)}
 div.historyItem-upload{background:#a6e4f7}div.historyItem-upload .state-icon{background-image:url(data_upload.gif)}
 div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px}
-div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}
-div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"}
-div.historyItem-new .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"}
+div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}div.historyItem-noPermission .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-noPermission .state-icon:before{content:"\f05e"}
+div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"}
+div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"}
 div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important}
 div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px}
 div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px}

diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/style/src/less/base.less
--- a/static/style/src/less/base.less
+++ b/static/style/src/less/base.less
@@ -1509,11 +1509,19 @@
     filter: alpha(opacity=60);
     -moz-opacity: .60;
     opacity: .60;
+    .state-icon {
+        line-height: 16px;
+        .fa-icon();
+        &:before {
+            content: "\f05e";
+        }
+    }
 }
 
 div.historyItem-paused {
     background: @state-paused-bg;
     .state-icon {
+        line-height: 16px;
         .fa-icon();
         &:before {
             content: "\f04c";
@@ -1523,6 +1531,7 @@
 
 div.historyItem-new {
     .state-icon {
+        line-height: 16px;
         .fa-icon();
         &:before {
             content: "\f071";

This diff is so big that we needed to truncate the remainder.

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