diff --git a/static/scripts/packed b/static/scripts/packed
new file mode 120000
index 00000000000..6a043149e81
--- /dev/null
+++ b/static/scripts/packed
@@ -0,0 +1 @@
+./
\ No newline at end of file
diff --git a/static/scripts/packed/galaxy.workflows.js b/static/scripts/packed/galaxy.workflows.js
deleted file mode 100644
index bdb3b57013c..00000000000
--- a/static/scripts/packed/galaxy.workflows.js
+++ /dev/null
@@ -1 +0,0 @@
-$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value;if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var h=galaxy_config.root+"api/tools";this.timer=setTimeout(function(){$.get(h,{q:g},function(j){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(j.length!=0){var i=$.map(j,function(l,k){return"link-"+l});$(i).each(function(k,l){$("[id='"+l+"']").parent().addClass("search_match");$("[id='"+l+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var m=$(this);var l=m.next();var k=true;while(l.length!==0&&l.hasClass("toolTitle")){if(l.is(":visible")){k=false;break}else{l=l.next()}}if(k){m.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},400)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(b,a){node=add_node("tool",a,b);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:b,_:"true"},global:false,dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status===0){c+=", server unavailable"}node.error(c)}})}function add_node_for_module(a,b){node=add_node(a,b);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b,a));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var o=n.match(c);if(o){d=d.concat(o)}})}});if(d){$.each(d,function(j,l){if($.inArray(l,b)===-1){b.push(l)}})}}});if(b&&b.length!==0){$.each(b,function(g,h){a+="<div>"+h.substring(2,h.length-1)+"</div>"});f.html(a);e.show()}else{f.html(a);e.hide()}}function show_form_for_tool(c,b){$(".right-content").hide();$("#right-content").show().html(c);if(b){$("#right-content").find(".toolForm:first").after("<p><div class='metadataForm'>             <div class='metadataFormTitle'>Edit Step Attributes</div>             <div class='form-row'>             <label>Annotation / Notes:</label>                     <div style='margin-right: 10px;'>                     <textarea name='annotation' rows='3' style='width: 100%'>"+b.annotation+"</textarea>                         <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div>                     </div>             </div>             </div>")}if(b&&b.type=="tool"){pjastr="<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'>             "+display_pja_list()+" <br/> "+display_file_list(b)+" <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>            </div><div class='form-row'>            <div style='margin-right: 10px;'><span id='pja_container'></span>";pjastr+="<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";$("#right-content").find(".toolForm").after(pjastr);for(var a in b.post_job_actions){if(a!="undefined"){display_pja(b.post_job_actions[a],b)}}$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(d){workflow.active_form_has_changes=false;b.update_field_data(d);show_workflow_parameters()},beforeSubmit:function(d){d.push({name:"tool_state",value:b.tool_state});d.push({name:"_",value:"true"})}}).each(function(){var d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">&#9660;</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/data.js b/static/scripts/packed/mvc/data.js
deleted file mode 100644
index 00ec3ccb6a4..00000000000
--- a/static/scripts/packed/mvc/data.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["mvc/ui/ui-modal","mvc/ui/ui-frames","mvc/ui/icon-button"],function(k,j,f){var h=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){if(!this.get("metadata")){this._set_metadata()}this.on("change",this._set_metadata,this)},_set_metadata:function(){var n=new h();_.each(_.keys(this.attributes),function(o){if(o.indexOf("metadata_")===0){var p=o.split("metadata_")[1];n.set(p,this.attributes[o]);delete this.attributes[o]}},this);this.set("metadata",n,{silent:true})},get_metadata:function(n){return this.attributes.metadata.get(n)},urlRoot:galaxy_config.root+"api/datasets"});var i=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(n){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var n=this,o=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:n.attributes.chunk_index++}).success(function(p){var q;if(p.ck_data!==""){q=p}else{n.attributes.at_eof=true;q=null}o.resolve(q)});return o}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(n){this.row_count=0;this.loading_chunk=false;new d({model:n.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(o){var n=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(n.model.get_next_chunk()).then(function(p){if(p){n._renderChunk(p);n.loading_chunk=false}n.loading_indicator.hide();n.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var r=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(r);var n=this.model.get_metadata("column_names"),s=$("<thead/>").appendTo(r),t=$("<tr/>").appendTo(s);if(n){t.append("<th>"+n.join("</th><th>")+"</th>")}else{for(var q=1;q<=this.model.get_metadata("columns");q++){t.append("<th>"+q+"</th>")}}var p=this,o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}else{$.when(p.model.get_next_chunk()).then(function(u){p._renderChunk(u)})}this.scroll_elt.scroll(function(){p.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(q,n,r){var o=$("<td>").text(q);var p=this.model.get_metadata("column_types");if(r!==undefined){o.attr("colspan",r).addClass("stringalign")}else{if(p){if(n<p.length){if(p[n]==="str"||p[n]==="list"){o.addClass("stringalign")}}}}return o},_renderRow:function(n){var o=n.split("\t"),q=$("<tr>"),p=this.model.get_metadata("columns");if(this.row_count%2!==0){q.addClass("dark_row")}if(o.length===p){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this)}else{if(o.length>p){_.each(o.slice(0,p-1),function(s,r){q.append(this._renderCell(s,r))},this);q.append(this._renderCell(o.slice(p-1).join("\t"),p-1))}else{if(p>5&&o.length===p-1){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this);q.append($("<td>"))}else{q.append(this._renderCell(n,0,p))}}}this.row_count++;return q},_renderChunk:function(n){var o=this.$el.find("table");_.each(n.ck_data.split("\n"),function(p,q){if(p!==""){o.append(this._renderRow(p))}},this)}});var g=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);scroll_elt=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var m=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:n.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(p){var s=parent.Galaxy;if(s&&s.modal){this.modal=s.modal}if(s&&s.frame){this.frame=s.frame}if(!this.modal||!this.frame){return}var o=p.model;var r=o.get("metadata");if(!o.get("file_ext")){return}this.file_ext=o.get("file_ext");if(this.file_ext=="bed"){if(r.get("chromCol")&&r.get("startCol")&&r.get("endCol")){this.col.chrom=r.get("chromCol")-1;this.col.start=r.get("startCol")-1;this.col.end=r.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function q(u,v){for(var t=0;t<v.length;t++){if(v[t].match(u)){return t}}return -1}this.col.chrom=q("Chrom",r.get("column_names"));this.col.start=q("Pos",r.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(o.id){this.dataset_id=o.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(o.get("url_viz")){this.url_viz=o.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(o.get("genome_build")){this.genome_build=o.get("genome_build")}var n=new f.IconButtonView({model:new f.IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(p.$el);this.$el.append(n.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(s){function r(x){return !isNaN(parseFloat(x))&&isFinite(x)}if(this.col.chrom===null){return}var w=$(s.target).parent();var t=w.children().eq(this.col.chrom).html();var n=w.children().eq(this.col.start).html();var p=this.col.end?w.children().eq(this.col.end).html():n;if(!t.match("^#")&&t!==""&&r(n)){var v={dataset_id:this.dataset_id,gene_region:t+":"+n+"-"+p};var q=w.offset();var o=q.left-10;var u=q.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:u+"px",left:o+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,v,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(n,q,p){var o=this;return function(){var r={};if(p){r["f-dbkey"]=p}$.ajax({url:n+"/list_tracks?"+$.param(r),dataType:"html",error:function(){o.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){o.modal.hide()}}})},success:function(s){o.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){o.modal.hide()},"View in saved visualization":function(){o.modal.show({title:"Add Data to Saved Visualization",body:s,buttons:{Cancel:function(){o.modal.hide()},"Add to visualization":function(){o.modal.hide();o.modal.$el.find("input[name=id]:checked").each(function(){var t=$(this).val();q.id=t;o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})})}}})},"View in new visualization":function(){o.modal.hide();o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})}}})}});return false}}});var l=function(q,o,r,n){var p=new o({model:new q(r)});p.render();if(n){n.append(p.$el)}return p};var c=function(p){if(!p.model){p.model=new i(p.dataset_config)}var o=p.parent_elt;var q=p.embedded;delete p.embedded;delete p.parent_elt;delete p.dataset_config;var n=(q?new m(p):new g(p));n.render();if(o){o.append(n.$el);n.expand_to_container()}return n};return{Dataset:b,TabularDataset:i,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/form/form-parameters.js b/static/scripts/packed/mvc/form/form-parameters.js
deleted file mode 100644
index e213405a8af..00000000000
--- a/static/scripts/packed/mvc/form/form-parameters.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(d,e,a,c,b){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(g,f){this.app=g},create:function(f){if(f.value===undefined){f.value=null}if(f.default_value===undefined){f.default_value=f.value}var h=null;var g=this.types[f.type];if(g&&typeof(this[g])==="function"){h=this[g].call(this,f)}if(!h){this.app.incompatible=true;if(f.options){h=this._fieldSelect(f)}else{h=this._fieldText(f)}console.debug("tools-form::_addRow() : Auto matched field type ("+f.type+").")}if(f.value!==undefined){h.value(f.value)}return h},_fieldData:function(f){if(!this.app.options.is_dynamic){f.info="Data input '"+f.name+"' ("+d.textify(f.extensions.toString())+")";f.value=null;return this._fieldHidden(f)}var g=this;return new a.View(this.app,{id:"field-"+f.id,extensions:f.extensions,optional:f.optional,multiple:f.multiple,type:f.type,data:f.options,onchange:function(){g.app.trigger("change")}})},_fieldSelect:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}if(f.type=="data_column"){f.error_text="Missing columns in referenced dataset."}var h=[];for(var j in f.options){var k=f.options[j];h.push({label:k[0],value:k[1]})}var l=e.Select;switch(f.display){case"checkboxes":l=e.Checkbox;break;case"radio":l=e.Radio;break}var g=this;return new l.View({id:"field-"+f.id,data:h,error_text:f.error_text||"No options available",optional:f.optional&&f.default_value===null,multiple:f.multiple,searchable:f.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}var g=this;return new e.Drilldown.View({id:"field-"+f.id,data:f.options,display:f.display,onchange:function(){g.app.trigger("change")}})},_fieldText:function(f){if(f.options){f.area=f.multiple;if(!d.validate(f.value)){f.value=""}else{if(f.value instanceof Array){f.value=value.toString()}else{f.value=String(f.value).replace(/[\[\]'"\s]/g,"");if(f.multiple){f.value=f.value.replace(/,/g,"\n")}}}}var g=this;return new e.Input({id:"field-"+f.id,area:f.area,onchange:function(){g.app.trigger("change")}})},_fieldSlider:function(f){var g=this;return new e.Slider.View({id:"field-"+f.id,precise:f.type=="float",min:f.min,max:f.max,onchange:function(){g.app.trigger("change")}})},_fieldHidden:function(f){return new e.Hidden({id:"field-"+f.id,info:f.info})},_fieldBoolean:function(f){var g=this;return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){g.app.trigger("change")}})},_fieldColor:function(f){var g=this;return new b({id:"field-"+f.id,onchange:function(){g.app.trigger("change")}})},_fieldLibrary:function(f){var g=this;return new c.View({id:"field-"+f.id,optional:f.optional,multiple:f.multiple,onchange:function(){g.app.trigger("change")}})}});return{View:View}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/form/form-select-content.js b/static/scripts/packed/mvc/form/form-select-content.js
deleted file mode 100644
index 9096af32ae1..00000000000
--- a/static/scripts/packed/mvc/form/form-select-content.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){history={};var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(this.template_batch());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(h){var f=this;function g(m,j){if(m){var n=[];for(var k in j){var l=j[k];n.push({label:l.hid+": "+l.name,value:l.id});history[l.id+"_"+l.src]=l}m.update(n)}}g(this.select_single,h.hda);g(this.select_multiple,h.hda);g(this.select_collection,h.hdca)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hdca"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=history[k[h]+"_"+this.list[this.current].type];if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=history[this._select().value()+"_hdca"];if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:d}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/history/history-contents.js b/static/scripts/packed/mvc/history/history-contents.js
deleted file mode 100644
index e51b069e137..00000000000
--- a/static/scripts/packed/mvc/history/history-contents.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.model.prototype.idAttribute="type_id";this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},isCopyable:function(i){var h=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return((_.isObject(i)&&i.id)&&(_.contains(h,i.model_class)))},copy:function(h){var m,i,l;if(_.isString(h)){m=h;l="hda";i="dataset"}else{m=h.id;l=({HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"})[h.model_class]||"hda";i=(l==="hdca"?"dataset_collection":"dataset")}var k=this,j=jQuery.post(this.url(),{content:m,source:l,type:i}).done(function(n){k.add([n])}).fail(function(o,n,p){k.trigger("error",k,j,{},"Error copying contents",{type:i,id:m,source:l})});return j},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(i,h){_.each(i,function(j){if(!j.type_id||!j.get("type_id")){j.type_id=g.typeIdStr(j.history_content_type,j.id)}});Backbone.Collection.prototype.set.call(this,i,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/history/history-model.js b/static/scripts/packed/mvc/history/history-model.js
deleted file mode 100644
index 3b86f23d76a..00000000000
--- a/static/scripts/packed/mvc/history/history-model.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/tools.js b/static/scripts/packed/mvc/tools.js
deleted file mode 100644
index 7f6e54890be..00000000000
--- a/static/scripts/packed/mvc/tools.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},urlRoot:galaxy_config.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C;if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){if(typeof ga!=="undefined"){ga("send","pageview",galaxy_config.root+"?q="+B)}$.get(A.urlRoot,{q:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/ui/ui-button-check.js b/static/scripts/packed/mvc/ui/ui-button-check.js
deleted file mode 100644
index 88a8d393bcf..00000000000
--- a/static/scripts/packed/mvc/ui/ui-button-check.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0,title:"Select/Unselect all"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement(this._template());this.$title=this.$(".title");this.$icon=this.$(".icon");this.value(this.options.value);this.$title.html(this.options.title);var b=this;this.$el.on("click",function(){b.current=(b.current===0&&2)||0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b,c){if(b!==undefined){if(c){if(b!==0){if(b!==c){b=1}else{b=2}}}this.current=b;this.$icon.removeClass().addClass("icon").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current},_template:function(){return'<div class="ui-button-check" ><span class="icon"/><span class="title"/></div>'}})});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/ui/ui-options.js b/static/scripts/packed/mvc/ui/ui-options.js
deleted file mode 100644
index 42c9eb9ce29..00000000000
--- a/static/scripts/packed/mvc/ui/ui-options.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){var h=this;this.optionsDefault={visible:true,data:[],id:c.uid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.all_button=new e({onclick:function(){h.$("input").prop("checked",h.all_button.value()!==0);h.trigger("change")}});this.$menu.append(this.all_button.$el)}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}this.on("change",function(){this.options.onchange&&this.options.onchange(this.value())})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h.trigger("change")});this.value(l);this.unwait()},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}var l=this._getValue();if(this.all_button){var k=l;if(!(k instanceof Array)){k=0}else{k=k.length}this.all_button.value(k,this._size())}return l},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input").first();if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){var h=this._size();if(h==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/ui/ui-select-default.js b/static/scripts/packed/mvc/ui/ui-select-default.js
deleted file mode 100644
index 7fa92e46cb7..00000000000
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-button-check"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(e){var d=this;this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){if(this.options.searchable){this.all_button=new b({onclick:function(){var f=[];if(d.all_button.value()!==0){f=d._availableOptions()}d.value(f);d.trigger("change")}});this.$el.prepend(this.all_button.$el)}this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}this.$select.on("change",function(){d.trigger("change")});this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(d){if(d!==undefined){if(d===null){d="__null__"}if(this.exists(d)||this.options.multiple){this.$select.val(d);if(this.$select.select2){this.$select.select2("val",d)}}}var e=this._getValue();if(this.all_button){this.all_button.value($.isArray(e)&&e.length||0,this._size())}return e},first:function(){var d=this.$select.find("option").first();if(d.length>0){return d.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},update:function(d){var f=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var e in d){this.$select.append(this._templateOption(d[e]))}if(this._size()==0){this.disable();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(f);if(this._getValue()===null&&!(this.options.multiple&&this.options.optional)){this.value(this.first())}},setOnChange:function(d){this.options.onchange=d},exists:function(d){return this.$select.find('option[value="'+d+'"]').length>0},_getValue:function(){var d=this.$select.val();if(!a.validate(d)){return null}return d},_availableOptions:function(){var d=[];this.$select.find("option").each(function(f,g){d.push($(g).attr("value"))});return d},_size:function(){return this.$select.find("option").length},_templateOption:function(d){return'<option value="'+d.value+'">'+d.label+"</option>"},_template:function(d){return'<div id="'+d.id+'" class="'+d.cls+'"><select id="'+d.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:c}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/ui/ui-select-library.js b/static/scripts/packed/mvc/ui/ui-select-library.js
deleted file mode 100644
index bf1f2b9446c..00000000000
--- a/static/scripts/packed/mvc/ui/ui-select-library.js
+++ /dev/null
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(e,g,b,a){var d=Backbone.Collection.extend({url:galaxy_config.root+"api/libraries"});var c=Backbone.Collection.extend({initialize:function(){var h=this;this.config=new Backbone.Model({library_id:null});this.config.on("change",function(){h.fetch({reset:true})})},url:function(){return galaxy_config.root+"api/libraries/"+this.config.get("library_id")+"/contents"}});var f=Backbone.View.extend({initialize:function(i){var h=this;this.libraries=new d();this.datasets=new c();this.options=i;this.library_select=new g.Select.View({optional:i.optional,onchange:function(j){h.datasets.config.set("library_id",j)}});this.dataset_select=new g.Select.View({optional:i.optional,multiple:i.multiple,onchange:function(){h.trigger("change")}});this.libraries.on("reset",function(){var j=[];h.libraries.each(function(k){j.push({value:k.id,label:k.get("name")})});h.library_select.update(j);h.trigger("change")});this.datasets.on("reset",function(){var k=[];var j=h.library_select.text();if(j!==null){h.datasets.each(function(l){if(l.get("type")==="file"){k.push({value:l.id,label:j+l.get("name")})}})}h.dataset_select.update(k);h.trigger("change")});this.on("change",function(){i.onchange&&i.onchange(h.value())});this.setElement(this._template());this.$(".library-select").append(this.library_select.$el);this.$(".dataset-select").append(this.dataset_select.$el);this.libraries.fetch({reset:true,success:function(){h.library_select.trigger("change");if(h.options.value!==undefined){h.value(h.options.value)}}})},value:function(h){return this.dataset_select.value()},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div><div class="dataset"><span class="dataset-title">Select Dataset</span><span class="dataset-select"/></div></div>'}});return{View:f}});
\ No newline at end of file