diff --git a/templates/dataset_code.tmpl b/templates/dataset_code.tmpl
deleted file mode 100644
index 9eb4ec545bd..00000000000
--- a/templates/dataset_code.tmpl
+++ /dev/null
@@ -1,156 +0,0 @@
-##
-## Render the dataset `$data`, using `$hid` as the displayed id
-##
-
-## separate so it's only called once
-#def render_script( $data )
-
-    <script type="text/javascript">
-    q( document ).ready( function() {
-        initShowHide( q );
-        ## This solves the problem of .hide() and .show() for the body div
-        ## not executing until after it's already rendered.
-        q( "div.ajaxHistoryItem" ).show()
-    })
-    </script>
-
-#end def
-
-## FIXME: This function is duplicated in history.tmpl!
-## This copy is used for rendering datasets when the client's javascript
-## is enabled.
-#def render_dataset( $data, $hid )
-
-    #if $data.state in ["no state","",None]:
-        #set $data_state = "queued"
-    #else
-        #set $data_state = $data.state
-    #end if
-
-    <div class="historyItemWrapper historyItem historyItem-$data_state ajaxHistoryItem" id="historyItem-$data.id" style="display:none;">
-        
-        ##
-        ## Header row for history items (name, state, action buttons)
-        ##
-        
-        <table cellpadding="0" cellspacing="0" border="0" width="100%">
-            <tr>
-                <td>
-                    <div style='padding-right: 5px; display: none;' id="progress-$data.id">
-                        <img src="$h.url_for('/static/style/data_running.gif')" border="0" align="middle" >
-                    </div>
-                    #if $data_state == 'running'
-                        <div style='padding-right: 5px;'><img src="$h.url_for('/static/style/data_running.gif')" border="0" align="middle"></div>
-                    #elif $data_state == 'ok'
-                        #pass
-                    #else
-                        #set $src = $h.url_for( "/static/style/data_%s.png" % $data_state )
-                        <div style='padding-right: 5px;'><img src="$src" border="0" align="middle"></div>
-                    #end if
-                </td>
-                <td>
-                    <div>
-                        <div style="float: right;"><a href="$h.url_for( controller='dataset', dataset_id=$data.id, action='display', filename='index')" target="_top"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
-                        <a href="edit?id=$data.id" target="galaxy_main"><img src="$h.url_for('/static/images/pencil_icon.png')" rollover="$h.url_for('/static/images/pencil_icon_dark.png')" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a>
-                        <a href="delete?id=$data.id" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="$h.url_for('/static/images/delete_icon.png')" rollover="$h.url_for('/static/images/delete_icon_dark.png')" width='16' height='16' alt='delete' class='deleteButton' border='0'></a>
-                        <!--
-                        $h.link_to_remote( "<img src='%s' rollover='%s' width='16' height='16' alt='delete' class='deleteButton' border='0'>" % ( $h.url_for('/static/images/delete_icon.png'), $h.url_for('/static/images/delete_icon_dark.png') ),
-                                           dict( url=$h.url( action="delete_async", id=$data.id ), 
-                                                 before=( "$( 'progress-%s' ).show()" % $data.id ),
-                                                 success=( "delete_item( 'historyItem-%s' )" % $data.id ),
-                                                 failure="alert( 'delete failed' )" ),
-                                           href="delete?id=%d" % $data.id,
-                                           title='delete this item' ) -->
-                        </div>
-                        <span class="historyItemTitle"><b>$hid: $data.display_name</b></span>
-                    </div>
-                </td>
-            </tr>
-        </table>
-        
-        ##
-        ## Body for history items, extra info and actions, data "peek"
-        ##
-        
-        <div id="info$data.id" class="historyItemBody">
-            #if $data_state == "queued"
-                <div>Job is waiting to run</div>
-            #elif $data_state == "running"
-                <div>Job is currently running</div>
-            #elif $data_state == "error"
-                <div>
-                    An error occurred running this job: <i>$data.display_info.strip()</i>, 
-                    <a href="${h.url_for( controller='dataset', action='errors', id=$data.id )}" target="galaxy_main">report this error</a>
-                </div>
-            #elif $data_state == "empty"
-                <div>No data: <i>$data.display_info</i></div>
-            #else
-                <div>
-                    $data.blurb,
-                    format: <span class="$data.ext">$data.ext</span>, 
-                    database:
-                    #if $data.dbkey == '?'
-                        <a href="edit?id=$data.id" target="galaxy_main"><span class="$data.dbkey">$data.dbkey</span></a>
-                    #else
-                        <span class="$data.dbkey">$data.dbkey</span>
-                    #end if
-                </div>
-                <div class="info">Info: $data.display_info </div>
-                <div> 
-                    #if $data.has_data:
-                        <a href="display?id=$data.id&tofile=yes&toext=$data.ext" target="_blank">save</a>
-                        #for $display_app in $data.datatype.get_display_types():
-                            #set $display_links = $data.datatype.get_display_links($data, $display_app, $app, $request.base)
-                            #if $len($display_links) > 0:
-                                | $data.datatype.get_display_label($display_app)
-                                    #for $display_name, $display_link in display_links:
-                                        <a target="_blank" href="$display_link">$display_name</a> 
-                                    #end for
-                            #end if
-                        #end for
-                    #end if
-                </div>
-                #if $data.peek != "no peek"
-                    <div><pre id="peek$data.id" class="peek">$data.display_peek</pre></div>
-                #end if
-            #end if
-               
-            ##  
-            ## Child datasets
-            ## 
-
-            #if $len( $data.children ) > 0:
-                #set $children = []
-                #for $child_assoc in $data.children:
-                    #if $child_assoc.child.visible:
-                        $children.append($child_assoc.child)
-                    #end if
-                #end for
-                #if $len( $children ) > 0:
-                    <div>
-                        There are ${len( $children )} secondary datasets.
-                        #for $idx, $child in $enumerate($children)
-                            $render_dataset( $child, $idx + 1 )
-                        #end for
-                    </div>
-                #end if
-            #end if
-
-        </div>
-    </div>
-    <script type="text/javascript">
-    q( document ).ready( function() {
-        showHideLink( q, $data.id );
-        deleteLink( q );
-    })
-    </script>
-
-#end def
-
-## this is necessary because this dataset remains in history.active_datasets
-## after deletion, until the history is reloaded
-## FIXME: still necessary now that we don't re-pull finished datasets?  test.
-#if $data.deleted is not True
-    $render_dataset( $data, $hid )
-    $render_script( $data )
-#end if
diff --git a/templates/dataset_state.tmpl b/templates/dataset_state.tmpl
deleted file mode 100644
index a6baf439a07..00000000000
--- a/templates/dataset_state.tmpl
+++ /dev/null
@@ -1 +0,0 @@
-$data.state
diff --git a/templates/history.tmpl b/templates/history.tmpl
deleted file mode 100644
index 4d6f4e296f4..00000000000
--- a/templates/history.tmpl
+++ /dev/null
@@ -1,418 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-
-<html>
-
-<head>
-<title>Galaxy History</title>
-
-## This is now only necessary for tests
-#set $running = bool ( [ data for data in $history.active_datasets if data.state in ['running', 'queued', '', None ] ] )
-#if $running
-<!-- running: do not change this comment, used by TwillTestCase.wait -->
-#end if
-
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<meta http-equiv="Pragma" content="no-cache">
-<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
-<link href="$h.url_for('/static/style/history.css')" rel="stylesheet" type="text/css" />
-
-
-## <!--[if lt IE 7]>
-## <script defer type="text/javascript" src="/static/scripts/ie_pngfix.js"></script>
-## <![endif]-->
-
-<script type="text/javascript" src="$h.url_for('/static/scripts/jquery.js')"></script>
-<script type="text/javascript" src="$h.url_for('/static/scripts/jquery.cookie.js')"></script>
-<script type="text/javascript" src="$h.url_for('/static/scripts/cookie_set.js')"></script>
-
-<script type="text/javascript">
-    var q = jQuery.noConflict();
-    q( document ).ready( function() {
-        initShowHide( q );
-        showHideLink( q, 'all' );
-        deleteLink( q );
-        // Collapse all
-        q("#top-links").append( "|&nbsp;" ).append( q("<a href='#'>collapse all</a>").click( function() {
-            q( "div.historyItemBody:visible" ).each( function() {
-                if ( q.browser.mozilla )
-                {
-                    q(this).find( "pre.peek" ).css( "overflow", "hidden" );
-                }
-                q(this).slideUp( "fast" );
-            })
-            var state = new CookieSet( "galaxy.history.expand_state" );
-            state.removeAll().save();
-        }))
-        // Add footer show / hide 
-        q( "div.footerheader" ).each( function() {
-            var menu = q(this).next();
-            menu.hide();
-            q(this).append( q("<a href='#'>options...</a>").click( function() {
-                if ( menu.is( ":visible" ) ) { menu.slideUp( "fast" ) }
-                else { menu.slideDown( "fast" ) } 
-            }))
-        })
-        // Links with confirmation
-        q( "a[@confirm]" ).click( function() {
-            return confirm( q(this).attr( "confirm"  ) )
-        })
-    })
-    // Functionized so AJAX'd datasets can call them
-    // Get shown/hidden state from cookie
-    function initShowHide( q ) {
-        q( "div.historyItemBody" ).hide();
-        // Load saved state and show as neccesary
-        var state = new CookieSet( "galaxy.history.expand_state" );
-	for ( id in state.store ) { q( "#" + id ).children( "div.historyItemBody" ).show(); }
-        // If Mozilla, hide scrollbars in hidden items since they cause animation bugs
-        if ( q.browser.mozilla ) {
-            q( "div.historyItemBody" ).each( function() {
-                if ( ! q(this).is( ":visible" ) ) q(this).find( "pre.peek" ).css( "overflow", "hidden" );
-            })
-        }
-        delete state;
-    }
-    // Add show/hide link
-    function showHideLink( q, data_id ) {
-        if ( data_id == "all" ) {
-            var element = "div.historyItemWrapper";
-        } else {
-            var element = "div#historyItem-" + data_id;
-        }
-        q( element ).each( function() {
-            var id = this.id;
-            var body = q(this).children( "div.historyItemBody" );
-            var peek = body.find( "pre.peek" )
-            q(this).children( "table" ).find( "span.historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() {
-                if ( body.is(":visible") ) {
-                    if ( q.browser.mozilla ) { peek.css( "overflow", "hidden" ) }
-                    body.slideUp( "fast" );
-                    ## other instances of this could be editing the cookie, refetch
-                    var state = new CookieSet( "galaxy.history.expand_state" );
-                    state.remove( id ); state.save();
-                    delete state;
-                } 
-                else {
-                    body.slideDown( "fast", function() { 
-                        if ( q.browser.mozilla ) { peek.css( "overflow", "auto" ); } 
-                    });
-                    var state = new CookieSet( "galaxy.history.expand_state" );
-                    state.add( id ); state.save();
-                    delete state;
-                }
-            })
-        })
-    }
-    // Add AJAX delete buttons
-    function deleteLink( q ) {
-        q( "a.historyItemDelete" ).each( function() {
-            var data_id = this.id.split( "-" )[1];
-            q(this).click( function() {
-                q( '#progress-' + data_id ).show();
-                q.ajax({
-                    url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ),
-                    error: function() { alert( "Delete failed" ) },
-                    success: function() { q( "#historyItem-" + data_id ).fadeOut( "fast", function() {
-                        q( "div#historyItemContainer-" + data_id ).remove();
-                        if ( q( "div.historyItemContainer" ).length < 1 ) {
-                            q ( "div#emptyHistoryMessage" ).show();
-                        }
-                    } ) }
-                })
-                return false;
-            })
-        })
-    }
-    // lifted from prototype.js
-    var \$A = Array.from = function(iterable) {
-        if (!iterable) return [];
-        if (iterable.toArray) {
-            return iterable.toArray();
-        } else {
-            var results = [];
-            for (var i = 0, length = iterable.length; i < length; i++)
-                results.push(iterable[i]);
-            return results;
-        }
-    }
-    Function.prototype.bind = function() {
-        var __method = this, args = \$A(arguments), object = args.shift();
-        return function() {
-            return __method.apply(object, args.concat(\$A(arguments)));
-        }
-    }
-    function updater( id, state_url, code_url, orig_state ) {
-        this.id = id;
-        this.state_url = state_url;
-        this.code_url = code_url;
-        this.old_state = orig_state;
-    }
-    updater.prototype.go = function() {
-        //Apparently IE doesn't do Array.indexOf...
-        //stop_states = new Array( "ok", "error" );
-        this.interval = setInterval( function() {
-            q.get(this.state_url, function(new_state) {
-                //if (stop_states.indexOf(new_state) >= 0) { clearInterval( this.interval ); }
-                if ((new_state == "ok") || (new_state == "error") || (new_state == "empty")) {
-                    clearInterval( this.interval );
-                }
-                if (this.old_state != new_state) {
-                    q( 'div#historyItemContainer-' + this.id ).load(this.code_url);
-                }
-                this.old_state = new_state;
-            }.bind(this) );
-        }.bind(this), 3000 );
-    }
-    updater.prototype.stop = function() {
-        clearInterval( this.interval );
-    }
-</script>
-
-<![if gte IE 7]>
-<script type="text/javascript">
-    q( document ).ready( function() {
-        // Add rollover effect to any image with a 'rollover' attribute
-        preload_images = {}
-        q( "img[@rollover]" ).each( function() {
-            var r = q(this).attr('rollover');
-            var s = q(this).attr('src');
-            preload_images[r] = true;
-            q(this).hover( 
-                function() { q(this).attr( 'src', r ) },
-                function() { q(this).attr( 'src', s ) }
-            )
-        })
-        for ( r in preload_images ) { q( "<img>" ).attr( "src", r ) }
-    })
-</script>
-<![endif]>
-
-<style type="text/css">
-#footer {
-    /* Netscape 4, IE 4.x-5.0/Win and other lesser browsers will use this */
-    position: absolute; left: 0px; bottom: 0px;
-}
-body > div#footer {
-    /* used by Opera 5+, Netscape6+/Mozilla, Konqueror, Safari, OmniWeb 4.5+, iCab, ICEbrowser */
-    position: fixed;
-}
-</style>
-
-<!--[if gte IE 5.5]>
-<![if lt IE 7]>
-<style type="text/css">
-div#footer {
-    /* IE5.5+/Win - this is more specific than the IE 5.0 version */
-    width:100%;
-    right: auto; bottom: auto;
-    left: expression( ( -5 - footer.offsetWidth + ( document.documentElement.clientWidth ? document.documentElement.clientWidth : document.body.clientWidth ) + ( ignoreMe2 = document.documentElement.scrollLeft ? document.documentElement.scrollLeft : document.body.scrollLeft ) ) + 'px' );
-    top: expression( ( - footer.offsetHeight + ( document.documentElement.clientHeight ? document.documentElement.clientHeight : document.body.clientHeight ) + ( ignoreMe = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop ) ) + 'px' );
-}
-</style>
-<![endif]>
-<![endif]-->
-
-</head>
-
-<body class="historyPage">
-
-<div id="top-links" class="historyLinks">
-    <a href="$h.url_for('history')">refresh</a> 
-</div>
-
-#if $history.deleted 
-    <div class="warningmessagesmall">
-        You are currently viewing a deleted history!
-    </div>
-    <p></p>
-#end if
-
-##
-## Render the dataset `$data`, using `$hid` as the displayed id
-##
-
-## FIXME: This function is duplicated in dataset_code.tmpl!
-## This copy is used for rendering datasets when the client's javascript
-## is NOT enabled.
-#def render_dataset( $data, $hid )
-
-    #if $data.state in ["no state","",None]:
-        #set $data_state = "queued"
-    #else
-        #set $data_state = $data.state
-    #end if
-    <div class="historyItemWrapper historyItem historyItem-$data_state" id="historyItem-$data.id">
-        
-        ##
-        ## Header row for history items (name, state, action buttons)
-        ##
-        
-        <table cellpadding="0" cellspacing="0" border="0" width="100%">
-            <tr>
-                <td>
-                    <div style='padding-right: 5px; display: none;' id="progress-$data.id">
-                        <img src="$h.url_for('/static/style/data_running.gif')" border="0" align="middle" >
-                    </div>
-                    #if $data_state == 'running'
-                        <div style='padding-right: 5px;'><img src="$h.url_for('/static/style/data_running.gif')" border="0" align="middle"></div>
-                    #elif $data_state == 'ok'
-                        #pass
-                    #else
-                        #set $src = $h.url_for( "/static/style/data_%s.png" % $data_state )
-                        <div style='padding-right: 5px;'><img src="$src" border="0" align="middle"></div>
-                    #end if
-                </td>
-                <td>
-                    <div style="overflow: hidden;">
-                        <div style="float: right;"><a href="$h.url_for( controller='dataset', dataset_id=$data.id, action='display', filename='index')" target="galaxy_main"><img src="$h.url_for('/static/images/eye_icon.png')" rollover="$h.url_for('/static/images/eye_icon_dark.png')" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a>
-                        <a href="edit?id=$data.id" target="galaxy_main"><img src="$h.url_for('/static/images/pencil_icon.png')" rollover="$h.url_for('/static/images/pencil_icon_dark.png')" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a>
-                        <a href="delete?id=$data.id" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="$h.url_for('/static/images/delete_icon.png')" rollover="$h.url_for('/static/images/delete_icon_dark.png')" width='16' height='16' alt='delete' class='deleteButton' border='0'></a>
-                        <!--
-                        $h.link_to_remote( "<img src='%s' rollover='%s' width='16' height='16' alt='delete' class='deleteButton' border='0'>" % ( $h.url_for('/static/images/delete_icon.png'), $h.url_for('/static/images/delete_icon_dark.png') ),
-                                           dict( url=$h.url( action="delete_async", id=$data.id ), 
-                                                 before=( "$( 'progress-%s' ).show()" % $data.id ),
-                                                 success=( "delete_item( 'historyItem-%s' )" % $data.id ),
-                                                 failure="alert( 'delete failed' )" ),
-                                           href="delete?id=%d" % $data.id,
-                                           title='delete this item' ) -->
-                        </div>
-                        <span class="historyItemTitle"><b>$hid: $data.display_name</b></span>
-                    </div>
-                </td>
-            </tr>
-        </table>
-        
-        ##
-        ## Body for history items, extra info and actions, data "peek"
-        ##
-        
-        <div id="info$data.id" class="historyItemBody">
-            #if $data_state == "queued"
-                <div>Job is waiting to run</div>
-            #elif $data_state == "running"
-                <div>Job is currently running</div>
-            #elif $data_state == "error"
-                <div>
-                    An error occurred running this job: <i>$data.display_info.strip()</i>, 
-                    <a href="${h.url_for( controller='dataset', action='errors', id=$data.id )}" target="galaxy_main">report this error</a>
-                </div>
-            #elif $data_state == "empty"
-                <div>No data: <i>$data.display_info</i></div>
-            #else
-                <div>
-                    $data.blurb,
-                    format: <span class="$data.ext">$data.ext</span>, 
-                    database:
-                    #if $data.dbkey == '?'
-                        <a href="edit?id=$data.id" target="galaxy_main"><span class="$data.dbkey">$data.dbkey</span></a>
-                    #else
-                        <span class="$data.dbkey">$data.dbkey</span>
-                    #end if
-                </div>
-                <div class="info">Info: $data.display_info </div>
-                <div> 
-                    #if $data.has_data:
-                        <a href="display?id=$data.id&tofile=yes&toext=$data.ext" target="_blank">save</a>
-                        #for $display_app in $data.datatype.get_display_types():
-                            #set $display_links = $data.datatype.get_display_links($data, $display_app, $app, $request.base)
-                            #if $len($display_links) > 0:
-                                | $data.datatype.get_display_label($display_app)
-                                    #for $display_name, $display_link in display_links:
-                                        <a target="_blank" href="$display_link">$display_name</a> 
-                                    #end for
-                            #end if
-                        #end for
-                    #end if
-                </div>
-                #if $data.peek != "no peek"
-                    <div><pre id="peek$data.id" class="peek">$data.display_peek</pre></div>
-                #end if
-            #end if
-               
-            ##  
-            ## Child datasets
-            ## 
-                              
-            #if $len( $data.children ) > 0:
-                #set $children = []
-                #for $child_assoc in $data.children:
-                    #if $child_assoc.child.visible:
-                        $children.append($child_assoc.child)
-                    #end if
-                #end for
-                #if $len( $children ) > 0:
-                    <div>
-                        There are ${len( $children )} secondary datasets.
-                        #for $idx, $child in $enumerate($children)
-                            $render_dataset( $child, $idx + 1 )
-                        #end for
-                    </div>
-                #end if
-            #end if
-
-        </div>
-    </div>
-
-#end def
-
-#if $len($history.active_datasets)<1
-    <div class="infomessagesmall" id="emptyHistoryMessage">
-#else    
-    ## Render all active (not deleted) datasets, ordered from newest to oldest
-    #for $data in reversed( $history.active_datasets )
-        #if $data.visible:
-            <div class="historyItemContainer" id="historyItemContainer-$data.id">
-                $render_dataset( $data, $data.hid )
-            </div>
-        #end if
-    #end for
-    <script type="text/javascript">
-    #for $data in reversed( $history.active_datasets )
-        #if $data.visible and $data.state not in [ "empty", "error", "ok" ]:
-            #set $state_url = $h.url_for( action='dataset_state', id=$data.id )
-            #set $code_url = $h.url_for( action='dataset_code', id=$data.id, hid=$data.hid )
-            var updater_${data.id} = new updater( $data.id, '$state_url', '$code_url', '$data.state' );
-            updater_${data.id}.go();
-        #end if
-    #end for
-    </script>
-    <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;">
-#end if
-        Your history is empty. Click 'Get Data' on the left pane to start
-    </div>
-
-</body>
-
-#if $app.config.get( "show_panel_footers", "true" ) == "true"
-<div style="height: 20px"></div>
-<div id="footer" >
-    <div class="footerheader">
-        <b>History</b> 
-    </div>
-    <div>
-        <div class="footermenu">
-            #if $t.user
-                <div style="padding-top: 5px;">
-                    #if $history.user
-                        <div class="footermenuitem">currently stored as "<a href="$h.url_for('/history_rename', id=$history.id )" target="galaxy_main">$history.name</a>"</div>
-                    #else
-                        <div class="footermenuitem"><a href="$h.url_for('/history_store')" target="galaxy_main">store</a> this history for later</div>
-                    #end if
-                    <div class="footermenuitem"><a href="$h.url_for('/history_available')" target="galaxy_main">view</a> previously stored histories</div>
-                    #if $len( $history.active_datasets ) > 0 and $history.user not in [ None , "" ]:
-                        <div class="footermenuitem"><a href="$h.url_for('/history_new')">create</a> a new empty history</div>
-                    #end if
-                </div>
-            #else
-                <div class="footermenumessage">
-                    <div class="infomark">You must be <a target="galaxy_main" href="$h.url_for('/user/login')">logged in</a> to store or switch histories.</div>
-                </div>
-            #end if
-            <div class="footermenuitem"><a href="$h.url_for('/history_share')" target="galaxy_main">share</a> current history</div>
-            <div class="footermenuitem"><a href="$h.url_for('/history_delete', id=$history.id )" confirm="Are you sure you want to delete the current history?">delete</a> current history</div>
-        </div>
-    </div>
-</div>
-#end if
-
-</html>