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'),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var g in this.list)this.$el.append(this.list[g].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
'}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
"),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(42),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){
+d.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,e){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()})},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},remove:function(t,e){var i=this;t=t||this.fxSpeed,this.$el.fadeOut(t,function(){a.View.prototype.remove.call(i),e&&e.call(i)})},render:function(t){return d.prototype.render.call(this,t)},_swapNewRender:function(t){return d.prototype._swapNewRender.call(this,t),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var t=this.model.get("state");if(t===e.NOT_VIEWABLE||t===e.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(t===e.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(t===e.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),t.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===e.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var t=d.prototype._renderDetails.call(this);return t.find(".actions .left").empty().append(this._renderSecondaryActions()),t.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),t.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(t),t},_renderSummary:function(){var t=this.model.toJSON(),e=this.templates.summaries[t.state];return(e=e||this.templates.summaries.unknown)(t,this)},_renderDetailMessages:function(){var t=this,e=r('
'),i=t.model.toJSON();return l.each(t.templates.detailMessages,function(n){e.append(r(n(i,t)))}),e},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case e.NOT_VIEWABLE:return[];case e.OK:case e.FAILED_METADATA:case e.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['',' "].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return r(['"].join("\n"))},events:l.extend(l.clone(d.prototype.events),{"click .display-btn":function(t){this.trigger("display",this,t)},"click .params-btn":function(t){this.trigger("params",this,t)},"click .download-btn":function(t){this.trigger("download",this,t)}}),toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetListItemView("+t+")"}});return h.prototype.templates=function(){var t=l.extend({},d.prototype.templates.warnings,{failed_metadata:n.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','',s("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'',s("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'',s("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'',s("This dataset has been deleted"),"
","<% } %>"])}),i=n.wrapTemplate(['','
','
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
',"<% if( dataset.peek ){ %>",'
<%= dataset.peek %> ',"<% } %>","<% } %>","
','
',s("You do not have permission to view this dataset"),"
","
','<%- dataset.misc_blurb %> ',"
","<% } %>","<% if( dataset.file_ext ){ %>",'','',s("format")," ",'<%- dataset.file_ext %> ',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'','',s("database")," ",'',"<%- dataset.metadata_dbkey %>"," ","
","<% } %>","<% if( dataset.misc_info ){ %>",'','<%- dataset.misc_info %> ',"
","<% } %>"],"dataset"),a[e.NEW]=n.wrapTemplate(["",s("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),a[e.NOT_VIEWABLE]=n.wrapTemplate(["",s("You do not have permission to view this dataset"),"
"],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["",s("The job creating this dataset was cancelled before completion"),"
"],"dataset"),a[e.QUEUED]=n.wrapTemplate(["",s("This job is waiting to run"),"
"],"dataset"),a[e.RUNNING]=n.wrapTemplate(["",s("This job is currently running"),"
"],"dataset"),a[e.UPLOAD]=n.wrapTemplate(["",s("This dataset is currently uploading"),"
"],"dataset"),a[e.SETTING_METADATA]=n.wrapTemplate(["",s("Metadata is being auto-detected"),"
"],"dataset"),a[e.PAUSED]=n.wrapTemplate(["",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),a[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","<%- dataset.misc_blurb %>
","<% } %>",'',s("An error occurred with this dataset"),": ",'<%- dataset.misc_info %>
'],"dataset"),a[e.EMPTY]=n.wrapTemplate(["",s("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),a.unknown=n.wrapTemplate(['Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'',s("The job creating this dataset has been resubmitted"),"
","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'','
<%- app.label %> ','
',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>"," ","
"),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("
").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(37),i(35),i(36)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=r.size(t.cache),l=0;ll?t.cache[l]:t.inputs);this.app.options.sustain_repeats&&o.hideOptions();var d=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(d.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("
").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(27)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('
'),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),"single"!=this.mode&&"multiple"!=this.mode||(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var g in this.list)this.$el.append(this.list[g].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode},template_batch:function(){return'
'}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
"),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(42),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){
n=[i(42),i(74),i(41),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){"use strict";var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('
'),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['"]),i={},n=t.wrapTemplate(['','
','
','<%- element.name %> ',"
",'
',"
']),o=t.wrapTemplate(['
']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['',"
"],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(57),i(7),i(40),i(20),i(18),i(29)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("
").append(s.help(t));if(t.citations){var i=o("
"),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(17),i(11),i(19)],s=function(t,e,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(t){this.set("value",parseFloat(t))}}),u=r.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});r.subModelTypes={integer:d,"float":h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new l(t.map(e.inputs,function(t){var e=r.subModelTypes[t.type]||r;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof f?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");if(t.append(S.tool_link(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a(" ','','
',"
"].join("")),tool_link:t.template(['
',"<% _.each( labels, function( label ){ %>",'',"<%- label %>"," ","<% }); %>"," ",'
',"<%- name %>"," "," <%- description %>"].join("")),tool_form:t.template(['
<%- tool.name %> (version <%- tool.version %>)
','
',"<% _.each( tool.inputs, function( input ){ %>",'
","<% }); %>","
",'
','
",'
"].join(""),{variable:"tool"})});return{ToolParameter:r,IntegerToolParameter:d,SelectToolParameter:u,Tool:p,ToolCollection:g,ToolSearch:v,ToolPanel:_,ToolPanelView:$,ToolFormView:E}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,function(t,e,i){var n,s;(function(i,o,a,r){n=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.size()||(this.$button=o("
")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return o(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var n=t.options[e];n.func&&o(this).children("a.popupmenu-option").click(function(e){n.func.call(t,e,n),e.preventDefault()})})}return this},template:function(t,e){return['"].join("")},_templateOptions:function(t){return t.length?a.map(t,function(t){if(t.divider)return'
';if(t.header)return['
',t.html," "].join("");var e=t.href||"javascript:void(0);",i=t.target?' target="'+t.target+'"':"",n=t.checked?'
':"";return['
"].join("")}).join(""):"
(no options) "},_getShownPosition:function(t){var e=this.$el.width(),i=t.pageX-e/2;return i=Math.min(i,o(document).scrollLeft()+o(window).width()-e-5),i=Math.max(i,o(document).scrollLeft()+5),{top:t.pageY,left:i}},_setUpCloseBehavior:function(){function t(t){if(o(document).off("click.close_popup"),window&&window.parent!==window)try{o(window.parent.document).off("click.close_popup")}catch(i){}else try{o("iframe#galaxy_main").contents().off("click.close_popup")}catch(i){}e.remove()}var e=this;if(o("html").one("click.close_popup",t),window&&window.parent!==window)try{o(window.parent.document).find("html").one("click.close_popup",t)}catch(i){}else try{o("iframe#galaxy_main").contents().one("click.close_popup",t)}catch(i){}},addItem:function(t,e){return e=e>=0?e:this.options.length,this.options.splice(e,0,t),this},removeItem:function(t){return t>=0&&this.options.splice(t,1),this},findIndexByHtml:function(t){for(var e=0;e
'},_templateContent:function(){return'
';
-},_templateBox:function(t){return'
'},_template:function(){return'
'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,n){var s,o;(function(a){s=[n(4),n(22)],o=function(t,e){var n=e.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.display,e.BaseIcons.prototype.initialize.call(this,t),this.initial=!0},value:function(t){var i=e.BaseIcons.prototype.value.call(this,t);if(this.initial&&null!==i&&this.header_index){this.initial=!1;var n=i;a.isArray(n)||(n=[n]);for(var s in n){var o=this.header_index[n[s]];for(var r in o)this._setState(o[r],!0)}}return i},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.fadeIn("fast"),i.removeClass("fa-plus-square"),i.addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square"),i.addClass("fa-plus-square"))},_templateOptions:function(e){function n(t,e){var i=t.find(".button-"+e);i.on("click",function(){o._setState(e,!i.data("is_expanded"))})}function s(e,r,l){l=l||[];for(i in r){var c=r[i],d=c.options.length>0,h=l.slice(0);o.header_index[c.value]=h.slice(0);var u=a("
");if(d){var p=t.uid(),g=a('
'),f=a('
');h.push(p);var m=a("
");m.append(g),m.append(o._templateOption({label:c.name,value:c.value})),u.append(m),s(f,c.options,h),u.append(f),n(u,p)}else u.append(o._templateOption({label:c.name,value:c.value}));e.append(u)}}var o=this;this.header_index={};var r=a("
");return s(r,e),r},_template:function(t){return'
'}});return{View:n}}.apply(e,s),!(void 0!==o&&(t.exports=o))}).call(e,n(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(13)],s=function(t,e){var i=o.View.extend({optionsDefault:{id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(i){var n=this;this.model=new o.Model,this.options=t.merge(i,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown"),this.$icon_dropdown.on("click",function(){n.$select.select2&&n.$select.select2("open")});var s=null;this.$(".icon-resize").on("mousedown",function(t){var e=t.pageY,i=n.$select.height();s=s||i,a("#dd-helper").show().on("mousemove",function(t){n.$select.height(Math.max(i+(t.pageY-e),s))}).on("mouseup mouseleave",function(){a("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new e.ButtonCheck({onclick:function(){var t=[];0!==n.all_button.value()&&(t=n._availableOptions()),n.value(t),n.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){n.trigger("change")}),this.on("change",function(){n.options.onchange&&n.options.onchange(this.value())})},value:function(t){void 0!==t&&(null===t&&(t="__null__"),(this.exists(t)||this.options.multiple)&&(this.$select.val(t),this.$select.select2&&this.$select.select2("val",t)));var e=this._getValue();return this.all_button&&this.all_button.value(a.isArray(e)&&e.length||0,this._size()),e},first:function(){var t=this.$select.find("option").first();return t.length>0?t.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(t,e){r.each(this.model.get("options"),function(e){!r.findWhere(t,e)&&t.push(e)}),e&&t.sort(e),this.update(t)},update:function(t){var e=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text})),this.model.set("options",t);for(var i in t)this.$select.append(this._templateOption(t[i]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(e),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(t){this.options.onchange=t},exists:function(t){return this.$select.find('option[value="'+t+'"]').length>0},_getValue:function(){var e=this.$select.val();return t.validate(e)?e:null},_availableOptions:function(){var t=[];return this.$select.find("option").each(function(e,i){t.push(a(i).attr("value"))}),t},_size:function(){return this.$select.find("option").length},_templateOption:function(t){return'
'+r.escape(t.label)+" "},_template:function(t){return'
'}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o){n=[i(4),i(21)],s=function(t,e){var i=o.View.extend({initialize:function(i){var n=this;this.ftpfile_list=new e.View({name:"file",optional:i.optional,multiple:i.multiple,onchange:function(){i.onchange&&i.onchange(n.value())}}),this.setElement(this.ftpfile_list.$el),t.get({url:Galaxy.root+"api/remote_files",success:function(t){var e=[];for(var i in t)e.push({value:t[i].path,label:t[i].path});n.ftpfile_list.update(e)}})},value:function(t){return this.ftpfile_list.value(t)}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o){n=[i(4),i(7),i(14),i(21)],s=function(t,e,i,n){var s=o.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),a=o.Collection.extend({initialize:function(){var t=this;this.config=new o.Model({library_id:null}),this.config.on("change",function(){t.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),r=o.View.extend({initialize:function(t){var i=this;this.libraries=new s,this.datasets=new a,this.options=t,this.library_select=new e.Select.View({onchange:function(t){i.datasets.config.set("library_id",t)}}),this.dataset_list=new n.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){i.trigger("change")}}),this.libraries.on("reset",function(){var t=[];i.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),i.library_select.update(t)}),this.datasets.on("reset",function(){var t=[],e=i.library_select.text();null!==e&&i.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),i.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(i.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){i.library_select.trigger("change"),void 0!==i.options.value&&i.value(i.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'
'}});return{View:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({initialize:function(e){var i=this;this.options=t.merge(e,{id:t.uid(),min:null,max:null,step:null,precise:!1,split:1e4}),this.setElement(this._template(this.options)),this.useslider=null!==this.options.max&&null!==this.options.min&&this.options.max>this.options.min,null===this.options.step&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(t,e){i.value(e.value)})):this.$(".ui-form-slider-text").css("width","100%"),this.$text=this.$("#text"),void 0!==this.options.value&&this.value(this.options.value);var n=[];this.$text.on("change",function(){i.value(a(this).val())}),this.$text.on("keyup",function(t){n[t.which]=!1,i.options.onchange&&i.options.onchange(a(this).val())}),this.$text.on("keydown",function(t){var e=t.which;n[e]=!0,i.options.is_workflow&&n[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&57>=e&&!n[16]||e>=96&&105>=e||(190==e||110==e)&&-1==a(this).val().indexOf(".")&&i.options.precise||(189==e||109==e)&&-1==a(this).val().indexOf("-")||i._isParameter(a(this).val())||n[91]||n[17]||event.preventDefault()})},value:function(t){return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),null!==this.options.max&&(t=Math.min(t,this.options.max)),null!==this.options.min&&(t=Math.max(t,this.options.min))),this.$slider&&this.$slider.slider("value",t),this.$text.val(t),this.options.onchange&&this.options.onchange(t)),this.$text.val()},_isParameter:function(t){return this.options.is_workflow&&"$"===String(t).substring(0,1)},_template:function(t){return'
'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i){n=[],s=function(){var t=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(t){this.clear().set(this.defaults).set(t)}}),e=i.Collection.extend({model:t});return{Model:t,Collection:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(e){var i=this,n=t.uid(),s=e.length>0;this.active[n]=!0;var o=a.Deferred();o.promise().always(function(){delete i.active[n],s&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+n)}),a.when(this.last).always(function(){i.active[n]?(s&&Galaxy.emit.debug("deferred::execute()","Running "+n),e(o),!s&&o.resolve()):o.reject()}),this.last=o.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var t in this.active)this.active[t]=!1},ready:function(){return a.isEmptyObject(this.active)}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,,,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(6),i(5),i(16)],s=function(t,e){var i=o.View.extend(t.LoggableMixin).extend(t.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(t){t=t||{},this.tooltipConfig=t.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(t.$activator,t)},render:function(){var t=this;return this.$el.html(this._template()),this.$el.find("[title]").tooltip(this.tooltipConfig),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(e){t.$annotation().text(e),t.model.save({annotation:e},{silent:!0}).fail(function(){t.$annotation().text(t.model.previous("annotation"))})}}),this},_template:function(){var t=this.model.get("annotation");return['
',e("Annotation")," ",'
',a.escape(t),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o){n=[i(77),i(31),i(30),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a="collections",r=t.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(t){r.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,this.panelStack=[],this.parentName=t.parentName,this.foldoutStyle=t.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(t){switch(t.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",t.get("element_type"))},_getItemViewOptions:function(t){var e=r.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(t){var e=this;return r.prototype._setUpItemViewListeners.call(e,t),e.listenTo(t,{"expanded:drilldown":function(t,e){this._expandDrilldownPanel(e)},"collapsed:drilldown":function(t,e){this._collapseDrilldownPanel(e)}}),this},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(t){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var t=n.wrapTemplate(['
','
",'
','
<%- collection.name || collection.element_identifier %>
','
','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),"<% } %>","
","
","
"],"collection");return o.extend(o.clone(r.prototype.templates),{controls:t})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(33),i(78),i(69),i(23),i(6),i(5)],s=function(t,e,n,s,r,l,c){"use strict";var d=e.DatasetListItemView,h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),this.hasUser=t.hasUser,this.purgeAllowed=t.purgeAllowed||!1,this.tagsEditorShown=t.tagsEditorShown||!1,this.annotationEditorShown=t.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===t.NOT_VIEWABLE?e:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===t.DISCARDED||!this.model.get("accessible"))return null;var e=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||e?(n.disabled=!0,e?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([t.UPLOAD,t.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var t=this,e=this.model.isDeletedOrPurged();return r({title:c(e?"Dataset is already deleted":"Delete"),disabled:e,faIcon:"fa-times",classes:"delete-btn",onclick:function(){t.$el.find(".icon-btn.delete-btn").trigger("mouseout"),t.model["delete"]()}})},_renderDetails:function(){var e=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([t.OK,t.FAILED_METADATA],i)&&(this._renderTags(e),this._renderAnnotation(e),this._makeDbkeyEditLink(e)),this._setUpBehaviors(e),e},_renderSecondaryActions:function(){var e=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case t.UPLOAD:case t.NEW:case t.NOT_VIEWABLE:return e;case t.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton()]);case t.OK:case t.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return e.concat([this._renderRerunButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var t=this.model.get("creating_job");return this.model.get("rerunnable")?r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(e){e.preventDefault(),!function(){var e=[i(19)];(function(e){var i=new e.View({job_id:t});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,e)}()}}):void 0},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(t))return null;if(!o.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var e=a(this.templates.visualizations(t,this));return e.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(e.find(".visualization-link").addBack(".visualization-link")),e},_addScratchBookFn:function(t){t.click(function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),t.preventDefault(),t.stopPropagation())})},_renderTags:function(t){if(this.hasUser){var e=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:t.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.tagsEditorShown=!0},onhide:function(){e.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(t.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(t){if(this.hasUser){var e=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:t.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.annotationEditorShown=!0},onhide:function(){e.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(t.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(t){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var e=a('
? ').attr("href",this.model.urls.edit).attr("target",this.linkTarget);t.find(".dbkey .value").replaceWith(e)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(t){this.trigger("edit",this,t)},"click .delete-btn":function(t){this.trigger("delete",this,t)},"click .rerun-btn":function(t){this.trigger("rerun",this,t)},"click .report-err-btn":function(t){this.trigger("report-err",this,t)},"click .visualization-btn":function(t){this.trigger("visualize",this,t)},"click .dbkey a":function(t){this.trigger("edit",this,t)}}),_clickUndeleteLink:function(t){return this.model.undelete(),!1},_clickPurgeLink:function(t){return this.model.purge(),!1},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAEditView("+t+")"}});return h.prototype.templates=function(){var t=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',c("This dataset has been deleted"),'
',c("Undelete it")," ","<% if( view.purgeAllowed ){ %>",'
',c("Permanently remove it from disk")," ","<% } %>","
","<% } %>"],"dataset")}),e=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'
">',' ","<% } else { %>",'
","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:t,visualizations:e})}(),{DatasetListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="dataset",s=e.SearchableModelMixin,l=o.Model.extend(e.LoggableMixin).extend(e.mixin(s,{_logNamespace:n,defaults:{state:t.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,i){this.debug(this+"(Dataset).initialize",e,i),this.get("accessible")||this.set("state",t.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var t=this.get("id");if(!t)return{};var e={purge:"datasets/"+t+"/purge_async",display:"datasets/"+t+"/display/?preview=True",edit:"datasets/"+t+"/edit",download:"datasets/"+t+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+t,rerun:"tool_runner/rerun?id="+t,show_params:"datasets/"+t+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+t+"&metadata_name="};return a.each(e,function(t,i){e[i]=Galaxy.root+t}),this.urls=e,e},_setUpListeners:function(){this.on("change:state",function(t,e){this.log(this+" has changed state:",t,e),this.inReadyState()&&this.trigger("state:ready",t,e,this.previous("state"))}),this.on("change:id change:file_ext",function(t){this._generateUrls()})},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return a.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=a.contains(t.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return a.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var e=this;return o.Model.prototype.fetch.call(this,t).always(function(){e._generateUrls()})},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},purge:function(t){if(this.get("purged"))return r.when();t=t||{},t.url=this.urls.purge;var e=this,n=r.ajax(t);return n.done(function(t,i,n){e.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf(r)&&(a=r),n.responseText=a,e.trigger("error",e,n,t,i(a),{error:a})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t='"'+this.get("name")+'",'+t),"Dataset("+t+")"}})),c=o.Collection.extend(e.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(t){return this.filter(function(e){return e.matches(t)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(33),i(6),i(5)],s=function(t,e,i){"use strict";var n=t.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(t,e){n.prototype.initialize.call(this,t,e)},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAListItemView("+t+")"}});return s.prototype.templates=function(){var t=e.wrapTemplate(['
','
','
','<%- dataset.hid %> ','<%- dataset.name %> ',"
","
"],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:e.wrapTemplate(["<% if( !dataset.visible ){ %>",'
',i("This dataset has been hidden"),"
","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:t,warnings:s})}(),{HDAListItemView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(72),i(42),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.DatasetAssociation,a=e.HistoryContentMixin,r=s.extend(i.mixin(a,{constructor:function(t,e){a.constructor.call(this,t,e)},defaults:o.extend({},s.prototype.defaults,a.defaults,{model_class:"HistoryDatasetAssociation"}),initialize:function(t,e){s.prototype.initialize.call(this,t,e),a.initialize.call(this,t,e)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HDA("+t+")"}}));return{HistoryDatasetAssociation:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(12),i(30),i(70),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a=e.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(t,e){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(e){a.prototype._swapNewRender.call(this,e);var i=this.model.get("populated")?t.OK:t.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDCAListItemView("+t+")"}});return r.prototype.templates=function(){var t=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'
',s("This collection has been hidden"),"
","<% } %>"],"collection")}),e=n.wrapTemplate(['
','
','
','<%- collection.hid %> ','<%- collection.name %> ',"
",'
',"
"],"collection");return o.extend({},a.prototype.templates,{warnings:t,titleBar:e})}(),{HDCAListItemView:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(43),i(4),i(6),i(5)],s=function(t,e,i,n){"use strict";var s="history",l=o.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{_logNamespace:s,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1},urlRoot:Galaxy.root+"api/histories",initialize:function(e,i,n){n=n||{},this.logger=n.logger||null,this.log(this+".initialize:",e,i,n),this.log("creating history contents:",i),this.contents=new t.HistoryContents(i||[],{historyId:this.get("id")}),this._setUpListeners(),this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(t,e,i,n,s){this.errorHandler(t,e,i,n,s)}),this.contents&&this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(a.makeArray(arguments)))}),this.on("change:id",function(t,e){this.contents&&(this.contents.historyId=e)})},errorHandler:function(t,e,i,n,s){this.clearUpdateTimeout()},nice_size:function(){return e.bytesToString(this.get("size"),!0,2)},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return Galaxy&&Galaxy.user?Galaxy.user.isAnonymous()||Galaxy.user.id!==this.get("user_id")?!1:!0:!1},contentsCount:function(){return r.reduce(r.values(this.get("state_details")),function(t,e){return t+e;
+},_templateBox:function(t){return'
'},_template:function(){return'
'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,n){var s,o;(function(a){s=[n(4),n(22)],o=function(t,e){var n=e.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.display,e.BaseIcons.prototype.initialize.call(this,t),this.initial=!0},value:function(t){var i=e.BaseIcons.prototype.value.call(this,t);if(this.initial&&null!==i&&this.header_index){this.initial=!1;var n=i;a.isArray(n)||(n=[n]);for(var s in n){var o=this.header_index[n[s]];for(var r in o)this._setState(o[r],!0)}}return i},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.fadeIn("fast"),i.removeClass("fa-plus-square"),i.addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square"),i.addClass("fa-plus-square"))},_templateOptions:function(e){function n(t,e){var i=t.find(".button-"+e);i.on("click",function(){o._setState(e,!i.data("is_expanded"))})}function s(e,r,l){l=l||[];for(i in r){var c=r[i],d=c.options.length>0,h=l.slice(0);o.header_index[c.value]=h.slice(0);var u=a("
");if(d){var p=t.uid(),g=a('
'),f=a('
');h.push(p);var m=a("
");m.append(g),m.append(o._templateOption({label:c.name,value:c.value})),u.append(m),s(f,c.options,h),u.append(f),n(u,p)}else u.append(o._templateOption({label:c.name,value:c.value}));e.append(u)}}var o=this;this.header_index={};var r=a("
");return s(r,e),r},_template:function(t){return'
'}});return{View:n}}.apply(e,s),!(void 0!==o&&(t.exports=o))}).call(e,n(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(13)],s=function(t,e){var i=o.View.extend({optionsDefault:{id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(i){var n=this;this.model=new o.Model,this.options=t.merge(i,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown"),this.$icon_dropdown.on("click",function(){n.$select.select2&&n.$select.select2("open")});var s=null;this.$(".icon-resize").on("mousedown",function(t){var e=t.pageY,i=n.$select.height();s=s||i,a("#dd-helper").show().on("mousemove",function(t){n.$select.height(Math.max(i+(t.pageY-e),s))}).on("mouseup mouseleave",function(){a("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new e.ButtonCheck({onclick:function(){var t=[];0!==n.all_button.value()&&(t=n._availableOptions()),n.value(t),n.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){n.trigger("change")}),this.on("change",function(){n.options.onchange&&n.options.onchange(this.value())})},value:function(t){void 0!==t&&(null===t&&(t="__null__"),(this.exists(t)||this.options.multiple)&&(this.$select.val(t),this.$select.select2&&this.$select.select2("val",t)));var e=this._getValue();return this.all_button&&this.all_button.value(a.isArray(e)&&e.length||0,this._size()),e},first:function(){var t=this.$select.find("option").first();return t.length>0?t.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(t,e){r.each(this.model.get("options"),function(e){!r.findWhere(t,e)&&t.push(e)}),e&&t.sort(e),this.update(t)},update:function(t){var e=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text})),this.model.set("options",t);for(var i in t)this.$select.append(this._templateOption(t[i]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(e),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(t){this.options.onchange=t},exists:function(t){return this.$select.find('option[value="'+t+'"]').length>0},_getValue:function(){var e=this.$select.val();return t.validate(e)?e:null},_availableOptions:function(){var t=[];return this.$select.find("option").each(function(e,i){t.push(a(i).attr("value"))}),t},_size:function(){return this.$select.find("option").length},_templateOption:function(t){return'
'+r.escape(t.label)+" "},_template:function(t){return'
'}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o){n=[i(4),i(21)],s=function(t,e){var i=o.View.extend({initialize:function(i){var n=this;this.ftpfile_list=new e.View({name:"file",optional:i.optional,multiple:i.multiple,onchange:function(){i.onchange&&i.onchange(n.value())}}),this.setElement(this.ftpfile_list.$el),t.get({url:Galaxy.root+"api/remote_files",success:function(t){var e=[];for(var i in t)e.push({value:t[i].path,label:t[i].path});n.ftpfile_list.update(e)}})},value:function(t){return this.ftpfile_list.value(t)}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o){n=[i(4),i(7),i(14),i(21)],s=function(t,e,i,n){var s=o.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),a=o.Collection.extend({initialize:function(){var t=this;this.config=new o.Model({library_id:null}),this.config.on("change",function(){t.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),r=o.View.extend({initialize:function(t){var i=this;this.libraries=new s,this.datasets=new a,this.options=t,this.library_select=new e.Select.View({onchange:function(t){i.datasets.config.set("library_id",t)}}),this.dataset_list=new n.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){i.trigger("change")}}),this.libraries.on("reset",function(){var t=[];i.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),i.library_select.update(t)}),this.datasets.on("reset",function(){var t=[],e=i.library_select.text();null!==e&&i.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),i.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(i.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){i.library_select.trigger("change"),void 0!==i.options.value&&i.value(i.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'
'}});return{View:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({initialize:function(e){var i=this;this.options=t.merge(e,{id:t.uid(),min:null,max:null,step:null,precise:!1,split:1e4}),this.setElement(this._template(this.options)),this.useslider=null!==this.options.max&&null!==this.options.min&&this.options.max>this.options.min,null===this.options.step&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(t,e){i.value(e.value)})):this.$(".ui-form-slider-text").css("width","100%"),this.$text=this.$("#text"),void 0!==this.options.value&&this.value(this.options.value);var n=[];this.$text.on("change",function(){i.value(a(this).val())}),this.$text.on("keyup",function(t){n[t.which]=!1,i.options.onchange&&i.options.onchange(a(this).val())}),this.$text.on("keydown",function(t){var e=t.which;n[e]=!0,i.options.is_workflow&&n[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&57>=e&&!n[16]||e>=96&&105>=e||(190==e||110==e)&&-1==a(this).val().indexOf(".")&&i.options.precise||(189==e||109==e)&&-1==a(this).val().indexOf("-")||i._isParameter(a(this).val())||n[91]||n[17]||event.preventDefault()})},value:function(t){return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),null!==this.options.max&&(t=Math.min(t,this.options.max)),null!==this.options.min&&(t=Math.max(t,this.options.min))),this.$slider&&this.$slider.slider("value",t),this.$text.val(t),this.options.onchange&&this.options.onchange(t)),this.$text.val()},_isParameter:function(t){return this.options.is_workflow&&"$"===String(t).substring(0,1)},_template:function(t){return'
'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i){n=[],s=function(){var t=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(t){this.clear().set(this.defaults).set(t)}}),e=i.Collection.extend({model:t});return{Model:t,Collection:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(e){var i=this,n=t.uid(),s=e.length>0;this.active[n]=!0;var o=a.Deferred();o.promise().always(function(){delete i.active[n],s&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+n)}),a.when(this.last).always(function(){i.active[n]?(s&&Galaxy.emit.debug("deferred::execute()","Running "+n),e(o),!s&&o.resolve()):o.reject()}),this.last=o.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var t in this.active)this.active[t]=!1},ready:function(){return a.isEmptyObject(this.active)}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,,,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(6),i(5),i(16)],s=function(t,e){var i=o.View.extend(t.LoggableMixin).extend(t.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(t){t=t||{},this.tooltipConfig=t.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(t.$activator,t)},render:function(){var t=this;return this.$el.html(this._template()),this.$el.find("[title]").tooltip(this.tooltipConfig),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(e){t.$annotation().text(e),t.model.save({annotation:e},{silent:!0}).fail(function(){t.$annotation().text(t.model.previous("annotation"))})}}),this},_template:function(){var t=this.model.get("annotation");return['
',e("Annotation")," ",'
',a.escape(t),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o){n=[i(77),i(31),i(30),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a="collections",r=t.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(t){r.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,this.panelStack=[],this.parentName=t.parentName,this.foldoutStyle=t.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(t){switch(t.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",t.get("element_type"))},_getItemViewOptions:function(t){var e=r.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(t){var e=this;return r.prototype._setUpItemViewListeners.call(e,t),e.listenTo(t,{"expanded:drilldown":function(t,e){this._expandDrilldownPanel(e)},"collapsed:drilldown":function(t,e){this._collapseDrilldownPanel(e)}}),this},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(t){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var t=n.wrapTemplate(['
','
",'
','
<%- collection.name || collection.element_identifier %>
','
','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),"<% } %>","
","
","
"],"collection");return o.extend(o.clone(r.prototype.templates),{controls:t})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(33),i(78),i(69),i(23),i(6),i(5)],s=function(t,e,n,s,r,l,c){"use strict";var d=e.DatasetListItemView,h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),this.hasUser=t.hasUser,this.purgeAllowed=t.purgeAllowed||!1,this.tagsEditorShown=t.tagsEditorShown||!1,this.annotationEditorShown=t.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===t.NOT_VIEWABLE?e:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===t.DISCARDED||!this.model.get("accessible"))return null;var e=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||e?(n.disabled=!0,e?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([t.UPLOAD,t.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var t=this,e=this.model.isDeletedOrPurged();return r({title:c(e?"Dataset is already deleted":"Delete"),disabled:e,faIcon:"fa-times",classes:"delete-btn",onclick:function(){t.$el.find(".icon-btn.delete-btn").trigger("mouseout"),t.model["delete"]()}})},_renderDetails:function(){var e=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([t.OK,t.FAILED_METADATA],i)&&(this._renderTags(e),this._renderAnnotation(e),this._makeDbkeyEditLink(e)),this._setUpBehaviors(e),e},_renderSecondaryActions:function(){var e=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case t.UPLOAD:case t.NEW:case t.NOT_VIEWABLE:return e;case t.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton()]);case t.OK:case t.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return e.concat([this._renderRerunButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var t=this.model.get("creating_job");return this.model.get("rerunnable")?r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(e){e.preventDefault(),!function(){var e=[i(19)];(function(e){var i=new e.View({job_id:t});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,e)}()}}):void 0},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(t))return null;if(!o.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var e=a(this.templates.visualizations(t,this));return e.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(e.find(".visualization-link").addBack(".visualization-link")),e},_addScratchBookFn:function(t){t.click(function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),t.preventDefault(),t.stopPropagation())})},_renderTags:function(t){if(this.hasUser){var e=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:t.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.tagsEditorShown=!0},onhide:function(){e.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(t.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(t){if(this.hasUser){var e=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:t.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.annotationEditorShown=!0},onhide:function(){e.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(t.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(t){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var e=a('
? ').attr("href",this.model.urls.edit).attr("target",this.linkTarget);t.find(".dbkey .value").replaceWith(e)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(t){this.trigger("edit",this,t)},"click .delete-btn":function(t){this.trigger("delete",this,t)},"click .rerun-btn":function(t){this.trigger("rerun",this,t)},"click .report-err-btn":function(t){this.trigger("report-err",this,t)},"click .visualization-btn":function(t){this.trigger("visualize",this,t)},"click .dbkey a":function(t){this.trigger("edit",this,t)}}),_clickUndeleteLink:function(t){return this.model.undelete(),!1},_clickPurgeLink:function(t){return this.model.purge(),!1},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAEditView("+t+")"}});return h.prototype.templates=function(){var t=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',c("This dataset has been deleted"),'
',c("Undelete it")," ","<% if( view.purgeAllowed ){ %>",'
',c("Permanently remove it from disk")," ","<% } %>","
","<% } %>"],"dataset")}),e=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'
">',' ","<% } else { %>",'
","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:t,visualizations:e})}(),{DatasetListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="dataset",s=e.SearchableModelMixin,l=o.Model.extend(e.LoggableMixin).extend(e.mixin(s,{_logNamespace:n,defaults:{state:t.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,i){this.debug(this+"(Dataset).initialize",e,i),this.get("accessible")||this.set("state",t.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var t=this.get("id");if(!t)return{};var e={purge:"datasets/"+t+"/purge_async",display:"datasets/"+t+"/display/?preview=True",edit:"datasets/"+t+"/edit",download:"datasets/"+t+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+t,rerun:"tool_runner/rerun?id="+t,show_params:"datasets/"+t+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+t+"&metadata_name="};return a.each(e,function(t,i){e[i]=Galaxy.root+t}),this.urls=e,e},_setUpListeners:function(){this.on("change:state",function(t,e){this.log(this+" has changed state:",t,e),this.inReadyState()&&this.trigger("state:ready",t,e,this.previous("state"))}),this.on("change:id change:file_ext",function(t){this._generateUrls()})},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return a.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=a.contains(t.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return a.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var e=this;return o.Model.prototype.fetch.call(this,t).always(function(){e._generateUrls()})},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},purge:function(t){if(this.get("purged"))return r.when();t=t||{},t.url=this.urls.purge;var e=this,n=r.ajax(t);return n.done(function(t,i,n){e.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf(r)&&(a=r),n.responseText=a,e.trigger("error",e,n,t,i(a),{error:a})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t='"'+this.get("name")+'",'+t),"Dataset("+t+")"}})),c=o.Collection.extend(e.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(t){return this.filter(function(e){return e.matches(t)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(33),i(6),i(5)],s=function(t,e,i){"use strict";var n=t.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(t,e){n.prototype.initialize.call(this,t,e)},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAListItemView("+t+")"}});return s.prototype.templates=function(){var t=e.wrapTemplate(['
','
','
','<%- dataset.hid %> ','<%- dataset.name %> ',"
","
"],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:e.wrapTemplate(["<% if( !dataset.visible ){ %>",'
',i("This dataset has been hidden"),"
","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:t,warnings:s})}(),{HDAListItemView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(72),i(42),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.DatasetAssociation,a=e.HistoryContentMixin,r=s.extend(i.mixin(a,{constructor:function(t,e){a.constructor.call(this,t,e)},defaults:o.extend({},s.prototype.defaults,a.defaults,{model_class:"HistoryDatasetAssociation"}),initialize:function(t,e){s.prototype.initialize.call(this,t,e),a.initialize.call(this,t,e)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HDA("+t+")"}}));return{HistoryDatasetAssociation:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(12),i(30),i(70),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a=e.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(t,e){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(e){a.prototype._swapNewRender.call(this,e);var i=this.model.get("populated")?t.OK:t.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDCAListItemView("+t+")"}});return r.prototype.templates=function(){var t=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'
',s("This collection has been hidden"),"
","<% } %>"],"collection")}),e=n.wrapTemplate(['
','
','
','<%- collection.hid %> ','<%- collection.name %> ',"
",'
',"
"],"collection");return o.extend({},a.prototype.templates,{warnings:t,titleBar:e})}(),{HDCAListItemView:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(43),i(4),i(6),i(5)],s=function(t,e,i,n){"use strict";var s="history",l=o.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{_logNamespace:s,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1},urlRoot:Galaxy.root+"api/histories",initialize:function(e,i,n){n=n||{},this.logger=n.logger||null,this.log(this+".initialize:",e,i,n),this.log("creating history contents:",i),this.contents=new t.HistoryContents(i||[],{historyId:this.get("id")}),this._setUpListeners(),this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(t,e,i,n,s){this.errorHandler(t,e,i,n,s)}),this.contents&&this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(a.makeArray(arguments)))}),this.on("change:id",function(t,e){this.contents&&(this.contents.historyId=e)})},errorHandler:function(t,e,i,n,s){this.clearUpdateTimeout()},nice_size:function(){return e.bytesToString(this.get("size"),!0,2)},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return Galaxy&&Galaxy.user?!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"):!1},contentsCount:function(){return r.reduce(r.values(this.get("state_details")),function(t,e){return t+e;
},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(t){return this.contents.running().length?this.setUpdateTimeout():(this.trigger("ready"),r.isFunction(t)&&t.call(this)),this},setUpdateTimeout:function(t){t=t||l.UPDATE_DELAY;var e=this;return this.clearUpdateTimeout(),this.updateTimeoutId=setTimeout(function(){e.refresh()},t),this.updateTimeoutId},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},refresh:function(t,e){t=t||[],e=e||{};var i=this;e.data=e.data||{},t.length&&(e.data.details=t.join(","));var n=this.contents.fetch(e);return n.done(function(t){i.checkForUpdates(function(){this.fetch()})}),n},_delete:function(t){return this.get("deleted")?a.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?a.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):a.when()},copy:function(t,e,i){if(t=void 0!==t?t:!0,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};t&&(n.current=!0),e&&(n.name=e),i||(n.all_datasets=!1);var s=this,o=a.post(this.urlRoot,n);return t?o.then(function(t){var e=new l(t);return e.setAsCurrent().done(function(){s.trigger("copied",s,t)})}):o.done(function(t){s.trigger("copied",s,t)})},setAsCurrent:function(){var t=this,e=a.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return e.done(function(){t.trigger("set-as-current",t)}),e},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));l.UPDATE_DELAY=4e3,l.getHistoryData=function(t,e){function i(e){return"current"===t?a.getJSON(Galaxy.root+"history/current_history_json"):a.ajax(Galaxy.root+"api/histories/"+t)}function n(t){return t&&t.empty}function s(t){if(n(t))return[];r.isFunction(o)&&(o=o(t)),r.isFunction(l)&&(l=l(t));var e={};return o.length&&(e.dataset_details=o.join(",")),l.length&&(e.dataset_collection_details=l.join(",")),a.ajax(Galaxy.root+"api/histories/"+t.id+"/contents",{data:e})}e=e||{};var o=e.detailIdsFn||[],l=e.hdcaDetailIds||[],c=a.Deferred(),d=null,h=e.historyFn||i,u=e.contentsFn||s,p=h(t);p.done(function(t){d=t,c.notify({status:"history data retrieved",historyJSON:d})}),p.fail(function(t,e,i){c.reject(t,"loading the history")});var g=p.then(u);return g.then(function(t){c.notify({status:"contents data retrieved",historyJSON:d,contentsJSON:t}),c.resolve(d,t)}),g.fail(function(t,e,i){c.reject(t,"loading the contents",{history:d})}),c};var c={fetch:function(t){return t=t||{},t.data=t.data||this._buildFetchData(t),t.traditional=!0,o.Collection.prototype.fetch.call(this,t)},_fetchOptions:["order","limit","offset","view","keys"],_buildFetchData:function(t){var e={},i=this._fetchDefaults();t=r.defaults(t||{},i),e=r.pick(t,this._fetchOptions);var n=r.has(t,"filters")?t.filters:i.filters||{};return r.isEmpty(n)||r.extend(e,this._buildFetchFilters(n)),e},_fetchDefaults:function(){return{}},_buildFetchFilters:function(t){var e={q:[],qv:[]};return r.each(t,function(t,i){t===!0&&(t="True"),t===!1&&(t="False"),e.q.push(i),e.qv.push(t)}),e}},d=o.Collection.extend(i.LoggableMixin).extend(c).extend({_logNamespace:s,model:l,DEFAULT_ORDER:"update_time",sortOrders:{update_time:{getter:function(t){return new Date(t.get("update_time"))},asc:!1},"update_time-asc":{getter:function(t){return new Date(t.get("update_time"))},asc:!0},name:{getter:function(t){return t.get("name")},asc:!0},"name-dsc":{getter:function(t){return t.get("name")},asc:!1},size:{getter:function(t){return t.get("size")},asc:!1},"size-asc":{getter:function(t){return t.get("size")},asc:!0}},initialize:function(t,e){e=e||{},this.log("HistoryCollection.initialize",arguments),this.includeDeleted=e.includeDeleted||!1,this.setOrder(e.order||this.DEFAULT_ORDER),this.currentHistoryId=e.currentHistoryId,this.allFetched=e.allFetched||!1,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},_fetchDefaults:function(){var t={order:this.order,view:"detailed"};return this.includeDeleted||(t.filters={deleted:!1,purged:!1}),t},setUpListeners:function(){this.on({"change:deleted":function(t){this.debug("change:deleted",this.includeDeleted,t.get("deleted")),!this.includeDeleted&&t.get("deleted")&&this.remove(t)},copied:function(t,e){this.setCurrent(new l(e,[]))},"set-as-current":function(t){var e=this.currentHistoryId;this.trigger("no-longer-current",e),this.currentHistoryId=t.id}})},sort:function(t){return t=t||{},this.setOrder(t.order),o.Collection.prototype.sort.call(this,t)},setOrder:function(t){var e=this,i=this.sortOrders[t];if(!r.isUndefined(i))return e.order=t,e.comparator=function(t,n){var s=e.currentHistoryId;return t.id===s?-1:n.id===s?1:(t=i.getter(t),n=i.getter(n),i.asc?t===n?0:t>n?1:-1:t===n?0:t>n?-1:1)},e.trigger("changed-order",e.order,e),e},fetch:function(t){if(t=t||{},this.allFetched)return a.when({});var e=this,i=r.defaults(t,{remove:!1,offset:e.length>=1?e.length-1:0,order:e.order}),n=t.limit;return r.isUndefined(n)||(i.limit=n),c.fetch.call(this,i).done(function(t){var i=r.isArray(t)?t.length:0;(!n||n>i)&&(e.allFetched=!0,e.trigger("all-fetched",e))})},create:function(t,e,i,n){var s=this,o=a.getJSON(Galaxy.root+"history/create_new_current");return o.done(function(t){s.setCurrent(new l(t,[],i||{}))})},setCurrent:function(t,e){return e=e||{},this.unshift(t,e),this.currentHistoryId=t.get("id"),e.silent||this.trigger("new-current",t,this),this},reset:function(t,e){return this.allFetched=!1,o.Collection.prototype.reset.call(this,t,e)},toString:function(){return"HistoryCollection("+this.length+")"}});return{History:l,HistoryCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(44),i(119),i(6),i(5),i(84)],s=function(t,e,i,n){"use strict";var s="list",l=o.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:t.ListItemView,collectionClass:o.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:n("This list is empty"),noneFoundMsg:n("No matching items found"),searchPlaceholder:n("search"),initialize:function(t,i){t=t||{},t.logger&&(this.logger=t.logger),this.log(this+".initialize:",t),this.fxSpeed=a.has(t,"fxSpeed")?t.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=t.searchFor||"",this.indicator=new e(this.$el),this.selecting=void 0!==t.selecting?t.selecting:!0,this.selected=t.selected||[],this.lastSelected=null,this.dragItems=t.dragItems||!1,this.viewClass=t.viewClass||this.viewClass,this.views=[],this.collection=t.collection||new this.collectionClass([]),this.filters=t.filters||[],this.$scrollContainer=t.$scrollContainer||this.$scrollContainer,this.title=t.title||"",this.subtitle=t.subtitle||"",this._setUpListeners()},freeViews:function(){return a.each(this.views,function(t){t.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on({error:function(t,e,i,n,s){console.error(t,e,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.logger&&this.on("all",function(t){this.log(this+"",arguments)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.listenTo(this.collection,{error:function(t,e,i,n,s){this.trigger("error",t,e,i,n,s)},reset:function(){this.renderItems()},add:this.addItemView,remove:this.removeItemView}),this.logger&&this.listenTo(this.collection,"all",function(t){this.info(this+"(collection)",arguments)}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(t,e){if(e&&e.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(t,i)}else e&&e.altKey&&!this.selecting&&this.showSelectors();this.selected.push(t.model.id),this.lastSelected=t.model.id},"view:de-selected":function(t,e){this.selected=a.without(this.selected,t.model.id)}})},render:function(t){this.log(this+".render",t);var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var t=r(this.templates.el({},this));return this._renderControls(t),this._renderTitle(t),this._renderSubtitle(t),this._renderSearch(t),this.renderItems(t),t},_renderControls:function(t){this.debug(this+"(ListPanel)._renderControls");var e=r(this.templates.controls({},this));return t.find(".controls").replaceWith(e),e},_renderTitle:function(t){},_renderSubtitle:function(t){},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;i.log("_queueNewRender:",t,e),r(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){i.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",this.className).append(t.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(t){return t=t||this.$el,t.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(t),this},_renderMultiselectActionMenu:function(t){t=t||this.$el;var e=t.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return e.empty();var s=r(['"].join("")),o=i.map(function(t){var e=['
',t.html," "].join("");return r(e).click(function(e){return e.preventDefault(),t.func(e)})});return s.find("ul").append(o),e.replaceWith(s),s},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(t){return(t||this.$el).find("> .list-items")},$messages:function(t){return(t||this.$el).find("> .controls .messages")},$emptyMessage:function(t){return(t||this.$el).find("> .empty-message")},renderItems:function(t){t=t||this.$el;var e=this;e.log(this+".renderItems",t);var i=e.$list(t);return e.views=e._filterCollection().map(function(t){return e._createItemView(t).render(0)}),i.empty(),e.views.length?(e._attachItems(t),e.$emptyMessage(t).hide()):e._renderEmptyMessage(t).show(),e.trigger("views:ready",e.views),e.views},_filterCollection:function(){var t=this;return t.collection.filter(a.bind(t._filterItem,t))},_filterItem:function(t){var e=this;return a.every(e.filters.map(function(e){return e.call(t)}))&&(!e.searchFor||t.matchesAll(e.searchFor))},_createItemView:function(t){var e=this._getItemViewClass(t),i=a.extend(this._getItemViewOptions(t),{model:t}),n=new e(i);return this._setUpItemViewListeners(n),n},_getItemViewClass:function(t){return this.viewClass},_getItemViewOptions:function(t){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:a.contains(this.selected,t.id),draggable:this.dragItems}},_setUpItemViewListeners:function(t){var e=this;return this.listenTo(t,"all",function(){var t=Array.prototype.slice.call(arguments,0);t[0]="view:"+t[0],e.trigger.apply(e,t)}),this.listenTo(t,"draggable:dragstart",function(t,e){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[e.model.toJSON()],t.dataTransfer.setData("text",JSON.stringify(i))},this),e},_attachItems:function(t){return this.$list(t).append(this.views.map(function(t){return t.$el})),this},_renderEmptyMessage:function(t){this.debug("_renderEmptyMessage",t,this.searchFor);var e=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(t).text(e)},expandAll:function(){a.each(this.views,function(t){t.expand()})},collapseAll:function(){a.each(this.views,function(t){t.collapse()})},addItemView:function(t,e,i){this.log(this+".addItemView:",t);var n=this;if(n._filterItem(t)){var s=n._createItemView(t);return r(s).queue("fx",[function(t){n.$emptyMessage().fadeOut(n.fxSpeed,t)},function(t){n._attachView(s),t()}]),s}},_attachView:function(t){var e=this;e.views.push(t),e.$list().append(t.render(0).$el.hide()),e.trigger("view:attached",t),t.$el.slideDown(e.fxSpeed,function(){e.trigger("view:attached:rendered")})},removeItemView:function(t,e,i){this.log(this+".removeItemView:",t);var n=this,s=n.viewFromModel(t);if(s)return n.views=a.without(n.views,s),n.trigger("view:removed",s),r({}).queue("fx",[function(t){s.$el.fadeOut(n.fxSpeed,t)},function(t){s.remove(),n.trigger("view:removed:rendered"),n.views.length?t():n._renderEmptyMessage().fadeIn(n.fxSpeed,t)}]),s},viewFromModelId:function(t){for(var e=0;e
i?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(t){return t.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:a.bind(this._firstSearch,this),onsearch:a.bind(this.searchItems,this),onclear:a.bind(this.clearSearch,this)}),t},_firstSearch:function(t){return this.log("onFirstSearch",t),this.searchItems(t)},searchItems:function(t){return this.searchFor=t,this.trigger("search:searching",t,this),this.renderItems(),this.$("> .controls .search-query").val(t),this},clearSearch:function(t){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTORS_AT:20,showSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.showSelector(t)})},hideSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.hideSelector(t)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(t){a.each(this.views,function(e){e.select(t)})},deselectAll:function(t){this.lastSelected=null,a.each(this.views,function(e){e.deselect(t)})},selectRange:function(t,e){var i=this.viewRange(t,e);return a.each(i,function(t){t.select()}),i},getSelectedViews:function(){return a.filter(this.views,function(t){return t.selected})},getSelectedModels:function(){return new this.collection.constructor(a.map(this.getSelectedViews(),function(t){return t.model}))},_showLoadingIndicator:function(t,i,n){this.debug("_showLoadingIndicator",this.indicator,t,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new e(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(t,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(t,e){this.debug("_hideLoadingIndicator",this.indicator,t,e),t=void 0!==t?t:this.fxSpeed,this.indicator&&this.indicator.hide(t,e)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(t,e){return e=e||0,this.$scrollContainer().animate({scrollTop:t},e),this},scrollToTop:function(t){return this.scrollTo(0,t)},scrollToItem:function(t,e){if(!t)return this;var i=t.el.offsetTop;return this.scrollTo(i,e)},scrollToId:function(t,e){return this.scrollToItem(this.viewFromModelId(t),e)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var t=i.wrapTemplate([""]),e=i.wrapTemplate(['','
",'
<%- view.subtitle %>
','
','
','
",'
','
','',n("All")," ",'',n("None")," ","
",'","
","
','
",'
<%- view.subtitle %>
','
','
','
",'
','
','',n("All")," ",'',n("None")," ","
",'","
","
',e("Tags")," ",'
'+e.path+' '+t.bytesToString(e.size)+' '+e.ctime+" Available files: Your FTP directory does not contain any files.
'},_template:function(){return'
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at '+this.options.ftp_upload_site+' using your Galaxy credentials (email address and password).
'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){return o.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(t){this.model=t.model,this.setElement(a("
").addClass("upload-settings")),this.$el.append(a("
").addClass("upload-settings-cover")),this.$el.append(a("
").addClass("upload-settings-table ui-table-striped").append("
")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var t=this;this.$table.empty(),r.each(this.options.parameters,function(e){var i=a("
").addClass("upload-"+e.id+" upload-icon-button fa").addClass(t.model.get(e.id)&&t.options.class_check||t.options.class_uncheck).on("click",function(){t.model.get("enabled")&&t.model.set(e.id,!t.model.get(e.id))});t.$table.append(a("
").append(a("
").append(i)).append(a("
").append(e.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},,,function(t,e,i){var n,s,o;(function(i,a){!function(i){s=[],n=i,o="function"==typeof n?n.apply(e,s):n,!(void 0!==o&&(t.exports=o))}(function(){i.fn.extend({hoverhighlight:function(t,e){return t=t||"body",this.size()?(a(this).each(function(){var i=a(this),n=i.data("target");n&&i.mouseover(function(i){a(n,t).css({background:e})}).mouseout(function(t){a(n).css({background:""})})}),this):this}})})}).call(e,i(1),i(1))},function(t,e,i){var n,s,o;(function(i,a){!function(i){s=[],n=i,o="function"==typeof n?n.apply(e,s):n,!(void 0!==o&&(t.exports=o))}(function(){function t(t,n){function s(t){var e=i(this).parent().children("input");e.focus().val("").trigger("clear:searchInput"),n.onclear()}function o(t,e){i(this).trigger("search:searchInput",e),"function"==typeof n.onfirstsearch&&f?(f=!1,n.onfirstsearch(e)):n.onsearch(e)}function r(){return['
"].join("")}function l(){return i(r()).focus(function(t){i(this).select()}).keyup(function(t){if(t.preventDefault(),t.stopPropagation(),i(this).val()||i(this).blur(),t.which===u&&n.escWillClear)s.call(this,t);else{var e=i(this).val();t.which===p||n.minSearchLen&&e.length>=n.minSearchLen?o.call(this,t,e):e.length||s.call(this,t)}}).on("change",function(t){o.call(this,t,i(this).val())}).val(n.initialVal)}function c(){return i(['
'].join("")).tooltip({placement:"bottom"}).click(function(t){s.call(this,t)})}function d(){return i(['
'].join("")).hide().tooltip({placement:"bottom"})}function h(){g.find(".search-loading").toggle(),g.find(".search-clear").toggle()}var u=27,p=13,g=i(t),f=!0,m={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(t){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.type(n)?("toggle-loading"===n&&h(),g):("object"===a.type(n)&&(n=a.extend(!0,{},m,n)),g.addClass("search-input").prepend([l(),c(),d()]))}var e=window._l||function(t){return t};a.fn.extend({searchInput:function(e){return this.each(function(){return t(this,e)})}})})}).call(e,i(1),i(1))},,function(t,e,i){var n,s;n=[],s=function(){function t(t,e){var i=/(-?[0-9\.]+)/g,n=t.toString().toLowerCase()||"",s=e.toString().toLowerCase()||"",o=String.fromCharCode(0),a=n.replace(i,o+"$1"+o).split(o),r=s.replace(i,o+"$1"+o).split(o),l=new Date(n).getTime(),c=l?new Date(s).getTime():null;if(c){if(c>l)return-1;if(l>c)return 1}for(var d,h,u=0,p=Math.max(a.length,r.length);p>u;u++){if(d=parseFloat(a[u])||a[u],h=parseFloat(r[u])||r[u],h>d)return-1;if(d>h)return 1}return 0}return t}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){(function(t,e){!function(i){t.event.props.push("dataTransfer"),i.uploadpost=function(e){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},e),s=n.data;if(s.error_message)return void n.error(s.error_message);var o=new FormData;for(var a in s.payload)o.append(a,s.payload[a]);var r=0;for(var a in s.files){var l=s.files[a];o.append(l.name,l.file,l.file.name),r+=l.file.size}return r>1048576*n.maxfilesize?void n.error(n.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",n.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var e=null;if(xhr.responseText)try{e=t.parseJSON(xhr.responseText)}catch(i){e=xhr.responseText}if(xhr.status<200||xhr.status>299){var s=xhr.statusText;403==xhr.status?s=n.error_login:0==xhr.status?s=n.error_server:s||(s=n.error_default),n.error(s+" ("+xhr.status+")")}else n.success(e)}},xhr.upload.addEventListener("progress",function(t){t.lengthComputable&&n.progress(Math.round(100*t.loaded/t.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",n),void xhr.send(o))},i.fn.uploadinput=function(t){var e=this,n=i.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},t),s=i('
");return e.append(s.change(function(t){n.onchange(t.target.files),i(this).val("")})),e.on("drop",function(t){n.ondragleave(t),t.dataTransfer&&(n.onchange(t.dataTransfer.files),t.preventDefault())}),e.on("dragover",function(t){t.preventDefault(),n.ondragover(t)}),e.on("dragleave",function(t){t.stopPropagation(),n.ondragleave(t)}),{dialog:function(){s.trigger("click")}}},i.fn.uploadbox=function(t){function n(t){if(t&&t.length&&!m){var i=g;return e.each(t,function(t,i){"new"!==t.mode&&e.filter(p,function(e){return e.name===t.name&&e.size===t.size}).length&&(t.duplicate=!0)}),e.each(t,function(t){if(!t.duplicate){var e=String(g++);p[e]=t,u.announce(e,p[e]),f++}}),i}}function s(t){p[t]&&(delete p[t],f--)}function o(){if(0==f||v)return v=!1,m=!1,void u.complete();m=!0;var t=-1;for(var e in p){t=e;break}p[t];s(t),i.uploadpost({url:u.url,data:u.initialize(t),success:function(e){u.success(t,e),o()},error:function(e){u.error(t,e),o()},progress:function(e){u.progress(t,e)}})}function a(){_.dialog()}function r(t){for(t in p)s(t)}function l(){m||(m=!0,o())}function c(){v=!0}function d(t){return u=i.extend({},u,t)}function h(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var u=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(t){},initialize:function(t){},progress:function(t,e){},success:function(t,e){},error:function(t,e){alert(e)},complete:function(){}},t),p={},g=0,f=0,m=!1,v=!1,_=i(this).uploadinput({multiple:!0,onchange:function(t){n(t)},ondragover:t.ondragover,ondragleave:t.ondragleave});return{select:a,add:n,remove:s,start:l,stop:c,reset:r,configure:d,compatible:h}}}(t)}).call(e,i(1),i(3))},function(t,e,i){var n=i(10).RightPanel,s=i(7),o=i(109);CurrentHistoryView=i(106).CurrentHistoryView,_l=i(5);var a=n.extend({title:_l("History"),initialize:function(t){n.prototype.initialize.call(this,t);var e=this;this.refreshButton=new s.ButtonLink({id:"history-refresh-button",title:_l("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){e.historyView.loadCurrentHistory()}}),this.optionsButton=new s.ButtonLink({id:"history-options-button",title:_l("History options"),
cls:"panel-header-button",icon:"fa fa-cog"}),this.viewMultiButton=null,t.userIsAnonymous||(this.viewMultiButton=new s.ButtonLink({id:"history-view-multi-button",title:_l("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:t.galaxyRoot+"history/view_multiple"})),this.optionsMenu=o(this.optionsButton.$el,{anonymous:t.userIsAnonymous,purgeAllowed:t.allow_user_dataset_purge,root:t.galaxyRoot}),this.historyView=new CurrentHistoryView({purgeAllowed:t.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}})},render:function(){n.prototype.render.call(this),this.$(".unified-panel-header").addClass("history-panel-header"),this.$(".panel-header-buttons").append([this.refreshButton.$el,this.optionsButton.$el,this.viewMultiButton?this.viewMultiButton.$el:null]),this.historyView.setElement(this.$(".history-panel"))},_templateBody:function(t){return['
"].join("")},toString:function(){return"HistoryPanel"}});t.exports=a},function(t,e,i){(function(e,n){var s=i(10).LeftPanel,o=i(46),a=i(115),r=i(5),l=s.extend({title:r("Tools"),initialize:function(t){s.prototype.initialize.call(this,t),this.log(this+".initialize:",t),this.stored_workflow_menu_entries=t.stored_workflow_menu_entries||[];var e=new o.ToolSearch({search_url:t.search_url,hidden:!1}),i=new o.ToolCollection(t.toolbox);this.tool_panel=new o.ToolPanel({tool_search:e,tools:i,layout:t.toolbox_in_panel}),this.tool_panel_view=new o.ToolPanelView({model:this.tool_panel}),this.uploadButton=new a({nginx_upload_path:t.nginx_upload_path,ftp_upload_site:t.ftp_upload_site,default_genome:t.default_genome,default_extension:t.default_extension})},render:function(){var t=this;s.prototype.render.call(t),t.$(".panel-header-buttons").append(t.uploadButton.$el),t.tool_panel.get("layout").size()>0&&(t.tool_panel_view.render(),t.$(".toolMenu").show()),t.$(".toolMenuContainer").prepend(t.tool_panel_view.$el),t._renderWorkflowMenu(),t.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint(e(t).attr("minsizehint"))})},_renderWorkflowMenu:function(){var t=this;t.$("#internal-workflows").append(t._templateTool({title:r("All workflows"),href:"workflow/list_for_run"})),n.each(t.stored_workflow_menu_entries,function(e){t.$("#internal-workflows").append(t._templateTool({title:e.stored_workflow.name,href:"workflow/run?id="+e.encoded_stored_workflow_id}))})},_templateTool:function(t){return['
"].join("")},_templateBody:function(){return['
','","
"].join("")},toString:function(){return"ToolPanel"}});t.exports=l}).call(e,i(1),i(3))},,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(30),i(71),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.DCListItemView,r=s.extend({initialize:function(t){s.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemEdit("+t+")"}}),l=t.DCEListItemView,c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemEdit("+t+")"}}),d=e.DatasetListItemEdit.extend({initialize:function(t){e.DatasetListItemEdit.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},_renderDeleteButton:function(){return null},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemEdit("+t+")"}});d.prototype.templates=function(){return a.extend({},e.DatasetListItemEdit.prototype.templates,{titleBar:t.DatasetDCEListItemView.prototype.templates.titleBar})}();var h=t.NestedDCDCEListItemView.extend({toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemEdit("+t+")"}});return{DCListItemEdit:r,DCEListItemEdit:c,DatasetDCEListItemEdit:d,NestedDCDCEListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(3))},function(t,e,i){var n,s;n=[i(70),i(31),i(99),i(6),i(5),i(16)],s=function(t,e,i,n,s){"use strict";var o=t.CollectionView,a=o.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,NestedDCDCEViewClass:i.NestedDCDCEListItemEdit,initialize:function(t){o.prototype.initialize.call(this,t)},_setUpBehaviors:function(t){if(t=t||this.$el,o.prototype._setUpBehaviors.call(this,t),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){var e=this,i="> .controls .name";t.find(i).attr("title",s("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(t){var n=e.model.get("name");t&&t!==n?(e.$el.find(i).text(t),e.model.save({name:t}).fail(function(){e.$el.find(i).text(e.model.previous("name"))})):e.$el.find(i).text(n)}})}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),r=a.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),l=r.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),c=l.extend({_setUpBehaviors:function(t){o.prototype._setUpBehaviors.call(this,t)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),d=a.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemEdit.extend({foldoutPanelClass:c}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:a,ListCollectionViewEdit:r,PairCollectionViewEdit:l,ListOfPairsCollectionViewEdit:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(122),i(86),i(32),i(6),i(5),i(83)],s=function(t,e,i,n,s){"use strict";function c(t){function e(){return i.length||(i=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),i}t=t||{},t.createPair=t.createPair||function(t){t=t||{};var e=t.listA.splice(t.indexA,1)[0],i=t.listB.splice(t.indexB,1)[0],n=t.listB.indexOf(e),s=t.listA.indexOf(i);return-1!==n&&t.listB.splice(n,1),-1!==s&&t.listA.splice(s,1),this._pair(e,i,{silent:!0})};var i=[];return t.preprocessMatch=t.preprocessMatch||function(t){var i=e.call(this);return a.extend(t,{matchTo:t.matchTo.name.replace(i[0],""),possible:t.possible.name.replace(i[1],"")})},function(e){this.debug("autopair _strategy ---------------------------"),e=e||{};var i,n=e.listA,s=e.listB,o=0,a={score:0,index:null},r=[];for(this.debug("starting list lens:",n.length,s.length),this.debug("bestMatch (starting):",JSON.stringify(a,null," "));o
=d?r.push(t.createPair.call(this,{listA:n,indexA:o,listB:s,indexB:a.index})):o+=1,!n.length||!s.length)return r}return this.debug("paired:",JSON.stringify(r,null," ")),this.debug("autopair _strategy ---------------------------"),r}}function d(t){var e=t.toJSON();return g(e,{historyId:t.historyId})}var h="collections",u=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"dataset paired",initialize:function(t){this.pair=t.pair||{}},template:a.template(['<%- pair.forward.name %> ','','<%- pair.name %> '," ",'<%- pair.reverse.name %> '].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(t){t.currentTarget.style.opacity="0.4",t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(t){t.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"PairView("+this.pair.name+")"}}),p=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(t){this.metric("PairedCollectionCreator.initialize",t),t=a.defaults(t,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=t.datasets,this.historyId=t.historyId,this.filters=this.commonFilters[t.filters]||this.commonFilters[this.DEFAULT_FILTERS],a.isArray(t.filters)&&(this.filters=t.filters),this.automaticallyPair=t.automaticallyPair,this.strategy=this.strategies[t.strategy]||this.strategies[this.DEFAULT_STRATEGY],a.isFunction(t.strategy)&&(this.strategy=t.strategy),this.matchPercentage=t.matchPercentage,this.twoPassAutopairing=t.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=t.oncancel,this.oncreate=t.oncreate,this.autoscrollDist=t.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(t){return t.sort(function(t,i){return e(t.name,i.name)}),t},_ensureIds:function(){return this.initialList.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.initialList},_splitByFilters:function(){function t(t,e){return e.test(t.name)}var e=this.filters.map(function(t){return new RegExp(t)}),i=[[],[]];return this.unpaired.forEach(function(n){e.forEach(function(e,s){t(n,e)&&i[s].push(n)})}),i},_addToUnpaired:function(t){var i=function(n,s){if(n===s)return n;var o=Math.floor((s-n)/2)+n,a=e(t.name,this.unpaired[o].name);if(0>a)return i(n,o);if(a>0)return i(o+1,s);for(;this.unpaired[o]&&this.unpaired[o].name===t.name;)o++;return o}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,t)},autoPair:function(t){var e=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:e[0],listB:e[1]}),e=this._splitByFilters()),t=t||this.strategy,e=this._splitByFilters(),i=i.concat(this[t].call(this,{listA:e[0],listB:e[1]}))},autopairSimple:c({scoreThreshold:function(){return 1},match:function(t){return t=t||{},t.matchTo===t.possible?{index:t.index,score:1}:t.bestMatch}}),autopairLevenshtein:c({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var i=t(e.matchTo,e.possible),n=1-i/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),autopairLCS:c({scoreThreshold:function(){return this.matchPercentage},match:function(t){t=t||{};var e=this._naiveStartingAndEndingLCS(t.matchTo,t.possible).length,i=e/Math.max(t.matchTo.length,t.possible.length);return i>t.bestMatch.score?{index:t.index,score:i}:t.bestMatch}}),_naiveStartingAndEndingLCS:function(t,e){for(var i="",n="",s=0,o=0;s=0&&o>=0&&t[s]===e[o];)n=[t[s],n].join(""),s-=1,o-=1;return i+n},_pair:function(t,e,i){i=i||{},this.debug("_pair:",t,e);var n=this._createPair(t,e,i.name);return this.paired.push(n),this.unpaired=a.without(this.unpaired,t,e),i.silent||this.trigger("pair:new",n),n},_createPair:function(t,e,i){if(!t||!e||t===e)throw new Error("Bad pairing: "+[JSON.stringify(t),JSON.stringify(e)]);return i=i||this._guessNameForPair(t,e),{forward:t,name:i,reverse:e}},_guessNameForPair:function(t,e,i){i=void 0!==i?i:this.removeExtensions;var n=t.name,s=e.name,o=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var a=o.lastIndexOf(".");if(a>0){var r=o.slice(a,o.length);o=o.replace(r,""),n=n.replace(r,""),s=s.replace(r,"")}}return o||n+" & "+s},_unpair:function(t,e){if(e=e||{},!t)throw new Error("Bad pair: "+JSON.stringify(t));return this.paired=a.without(this.paired,t),this._addToUnpaired(t.forward),this._addToUnpaired(t.reverse),e.silent||this.trigger("pair:unpair",[t]),t},unpairAll:function(){for(var t=[];this.paired.length;)t.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",t)},_pairToJSON:function(t,e){return e=e||"hda",{collection_type:"paired",src:"new_collection",name:t.name,element_identifiers:[{name:"forward",id:t.forward.id,src:e},{name:"reverse",id:t.reverse.id,src:e}]}},createList:function(t){var e=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",n={type:"dataset_collection",collection_type:"list:paired",name:a.escape(t||e.$(".collection-name").val()),element_identifiers:e.paired.map(function(t){return e._pairToJSON(t)})};return e.blocking=!0,r.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(n)}).always(function(){e.blocking=!1}).fail(function(t,i,n){e._ajaxErrHandler(t,i,n)}).done(function(t,i,n){e.trigger("collection:created",t,i,n),e.metric("collection:created",t),"function"==typeof e.oncreate&&e.oncreate.call(this,t,i,n)})},_ajaxErrHandler:function(t,e,i){this.error(t,e,i);var n=s("An error occurred while creating this collection");t&&(n+=0===t.readyState&&0===t.status?": "+s("Galaxy could not be reached and may be updating.")+s(" Try again in a few minutes."):t.responseJSON?""+JSON.stringify(t.responseJSON)+" ":": "+i),creator._showAlert(n,"alert-danger")},render:function(t,e){return this.$el.empty().html(p.templates.main()),this._renderHeader(t),this._renderMiddle(t),this._renderFooter(t),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(t,e){var i=this.$(".header").empty().html(p.templates.header()).find(".help-content").prepend(l(p.templates.helpContent()));return this._renderFilters(),i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(t,e){var i=this.$(".middle").empty().html(p.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),i},_renderUnpaired:function(t,e){var i,n,o=this,a=[],r=this._splitByFilters();return this.$(".forward-column .title").text([r[0].length,s("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[0].length)),this.$(".reverse-column .title").text([r[1].length,s("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=r[1].map(function(t,e){return void 0!==r[0][e]&&r[0][e]!==t&&a.push(o._renderPairButton()),o._renderUnpairedDataset(t)}),i=r[0].map(function(t){return o._renderUnpairedDataset(t)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(a)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(t){return["(",t," ",s("filtered out"),")"].join("")},_renderUnpairedDataset:function(t){return l("
').text("("+s("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(t),t},_renderUnpairedNotShown:function(){var t=l('
').text("("+s("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(t),t},_adjUnpairedOnScrollbar:function(){var t=this.$(".unpaired-columns").last(),e=this.$(".unpaired-columns .reverse-column .dataset").first();if(e.size()){var i=t.offset().left+t.outerWidth(),n=e.offset().left+e.outerWidth(),s=Math.floor(i)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",s>0?s:0)}},_renderPaired:function(t,e){if(this.$(".paired-column-title .title").text([this.paired.length,s("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(t,e){var n=new u({pair:t});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['',' "].join(""))})},_renderPairedEmpty:function(){var t=l('
').text("("+s("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(t),t},_renderFooter:function(t,e){var i=this.$(".footer").empty().html(p.templates.footer());return this.$(".remove-extensions").prop("checked",this.removeExtensions),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),i},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(t){function e(t,e){return['',s("Forward"),": ",t,", ",s("Reverse"),": ",e," "].join("")}var i=l(a.template(['','
',s("Choose from the following filters to change which unpaired reads are shown in the display"),":
",a.values(this.commonFilters).map(function(t){return e(t[0],t[1])}).join(""),"
');i.size()?i.before(n):e.append(n)},_checkForAutoscroll:function(t,e){var i=2,n=t.offset(),s=t.scrollTop(),o=e-n.top,a=n.top+t.outerHeight()-e;o>=0&&o=0&&at&&t>o-a)return s}return l()},_dropPairedColumns:function(t){t.preventDefault(),t.dataTransfer.dropEffect="move";var e=this._getNearestPairedDatasetLi(t.originalEvent.clientY);return e.size()?this.$dragging.insertBefore(e):this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last()),this._syncPairsToDom(),!1},_syncPairsToDom:function(){var t=[];this.$(".paired-columns .dataset.paired").each(function(){t.push(l(this).data("pair"))}),this.paired=t,this._renderPaired()},_pairDragstart:function(t,e){e.$el.addClass("selected");var i=this.$(".paired-columns .dataset.selected");this.$dragging=i},_pairDragend:function(t,e){l(".element-drop-placeholder").remove(),this.$dragging=null},toggleExtensions:function(t){var e=this;e.removeExtensions=void 0!==t?t:!e.removeExtensions,a.each(e.paired,function(t){t.customizedName||(t.name=e._guessNameForPair(t.forward,t.reverse))}),e._renderPaired(),e._renderFooter()},_changeName:function(t){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(t){13!==t.keyCode||this.blocking||this._clickCreate()},_getName:function(){return a.escape(this.$(".collection-name").val())},_clickCreate:function(t){var e=this._getName();e?this.blocking||this.createList():this._validationWarning("name")},_printList:function(t){var e=this;a.each(t,function(i){t===e.paired&&e._printPair(i)})},_printPair:function(t){this.debug(t.forward.name,t.reverse.name,": ->",t.name)},toString:function(){return"PairedCollectionCreator"}});p.templates=p.templates||{main:a.template(['','
','