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e=this._get_width(this.$el),i=this.$el.height(),n=this.options.container,s=this._get_width(n),o=this._get_height(n),a=n.position(),r=0,l=0;if(-1!=["top","bottom"].indexOf(t))switch(l=a.left-e+(s+e)/2,t){case"top":r=a.top-i-5;break;case"bottom":r=a.top+o+5}else switch(r=a.top-i+(o+i)/2,t){case"right":l=a.left+s}return{top:r,left:l}},_get_width:function(t){return t.width()+parseInt(t.css("padding-left"))+parseInt(t.css("padding-right"))},_get_height:function(t){return t.height()+parseInt(t.css("padding-top"))+parseInt(t.css("padding-bottom"))},_hide:function(t){r(this.options.container).is(t.target)||r(this.el).is(t.target)||0!==r(this.el).has(t.target).length||this.hide()},_template:function(t){var e='
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',"Warning: This is a experimental feature. Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' cite Galaxy.',"
"],"element");return o.extend({},e.DatasetListItemView.prototype.templates,{titleBar:t})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(t){c.prototype._swapNewRender.call(this,t);var e=this.model.get("state")||"ok";return this.$el.addClass("state-"+e),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+t+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(95),i(6),i(5)],s=function(t,e,i){var n="collections",s={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return o.extend(t,t.object,{element_id:t.id}),delete 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t=this.get("element_identifier");return["DatasetDCE(",t,")"].join("")}})),h=c.extend({model:d,initialize:function(t,e){this.debug(this+"(DatasetDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),u=a.Model.extend(e.LoggableMixin).extend(e.SearchableModelMixin).extend({_logNamespace:n,defaults:{collection_type:null,deleted:!1},collectionClass:c,initialize:function(t,e){this.debug(this+"(DatasetCollection).initialize:",t,e,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var t=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(t),this.elements},toJSON:function(){var t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(t){return this.elements},"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)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),p=u.extend({collectionClass:h,initialize:function(t,e){this.debug(this+"(ListDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),f=p.extend({initialize:function(t,e){this.debug(this+"(PairDatasetCollection).initialize:",t,e),p.prototype.initialize.call(this,t,e)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),g=u.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),m=c.extend({model:g,initialize:function(t,e){this.debug(this+"(NestedDCDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),v=f.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedPairDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",t,")"].join("")}})),_=m.extend({model:v,initialize:function(t,e){this.debug(this+"(NestedPairDCDCECollection).initialize:",t,e),m.prototype.initialize.call(this,t,e)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),y=u.extend({collectionClass:_,initialize:function(t,e){this.debug(this+"(ListPairedDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:p,PairDatasetCollection:f,ListPairedDatasetCollection:y}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(45),i(15),i(6),i(10),i(109),i(5),i(106)],s=function(t,e,i,n,s,c){function d(t){var e=t.toJSON(),i=g(e,{creationFn:function(e,i){return e=e.map(function(t){return{id:t.id,name:t.name,src:"dataset"===t.history_content_type?"hda":"hdca"}}),t.createHDCA(e,"list",i)}});return i}var h="collections",u=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"collection-element",initialize:function(t){this.element=t.element||{},this.selected=t.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name %>","",'"].join("")),select:function(t){this.$el.toggleClass("selected",t),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var t=this,e=this.$el.parent().width();this.$el.animate({"margin-right":e},"fast",function(){t.trigger("discard",{source:t}),t.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click 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element")+":",this.element.name));e&&(this.element.name=e,this.render())},_clickDiscard:function(t){t.stopPropagation(),this.discard()},_dragstart:function(t){t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(t){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"DatasetCollectionElementView()"}}),p=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,elementViewClass:u,collectionClass:t.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(t){this.metric("ListCollectionCreator.initialize",t);var e=this;a.each(this.defaultAttributes,function(i,n){i=t[n]||i,e[n]=i}),e.initialElements=t.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var t=this;return t.invalidElements=[],this.workingElements=this.workingElements.filter(function(e){var i=t._isElementInvalid(e);return i&&t.invalidElements.push({element:e,text:i}),!i}),this.workingElements},_isElementInvalid:function(t){return"dataset"!==t.history_content_type?c("is not a dataset"):t.state!==e.OK?c(a.contains(e.NOT_READY_STATES,t.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):t.deleted||t.purged?c("has been deleted or purged"):null},_mangleDuplicateNames:function(){var t=900,e=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+e+")",e+=1,e>=t)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(t){},render:function(t,e){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(t,e){var i=this,n=l(""),s=i.$list();a.each(this.elementViews,function(t){t.destroy(),i.removeElementView(t)}),i.workingElements.forEach(function(t){var e=i._createElementView(t);n.append(e.$el)}),i._renderClearSelected(),s.empty().append(n.children()),a.invoke(i.elementViews,"render"),s.height()>s.css("max-height")?s.css("border-width","1px 0px 1px 0px"):s.css("border-width","0px")},_createElementView:function(t){var e=new this.elementViewClass({element:t,selected:a.has(this.selectedIds,t.id)});return this.elementViews.push(e),this._listenToElementView(e),e},_listenToElementView:function(t){var e=this;e.listenTo(t,{select:function(t){var i=t.source.element;t.selected?e.selectedIds[i.id]=!0:delete e.selectedIds[i.id],e.trigger("elements:select",t)},discard:function(t){e.trigger("elements:discard",t)}})},addElementView:function(t){},removeElementView:function(t){delete this.selectedIds[t.element.id],this._renderClearSelected(),this.elementViews=a.without(this.elementViews,t),this.stopListening(t)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(t){return t},createList:function(t){if(!this.workingElements.length){var e=c("No valid elements for final list")+". 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","
",c(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
","
",c(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
","
",c(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
","
",c(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
","
",c(['Click the "Cancel" button to exit the interface.'].join("")),"
","
","
",c(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
"].join("")),invalidElements:a.template([c("The following selections could not be included due to problems:"),"
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","
",'"].join(""))},toString:function(){return"ListCollectionCreator"}}),f=function(t,e,i){var s,o=l.Deferred(),r=Galaxy.modal||new n.View;return e=a.defaults(e||{},{elements:t,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(t,e){r.hide(),o.resolve(e)}}),s=new i(e),r.show({title:e.title||c("Create a collection"),body:s.$el,width:"80%",height:"min-content",closing_events:!0}),s.render(),window._collectionCreator=s,o},g=function(t,e){return e=e||{},e.title=c("Create a collection from a list of datasets"),f(t,e,p)};return{DatasetCollectionElementView:u,ListCollectionCreator:p,collectionCreatorModal:f,listCollectionCreatorModal:g,createListCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(48),i(15),i(26),i(6),i(5)],s=function(t,e,i,n,s){var c="dataset",d=t.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log(this+".initialize:",t),d.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this),
this.model.on("change",function(t,e){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_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.add_dataset(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(['
"}})}.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),i(7),i(43),i(57),i(56),i(53)],s=function(t,e,i,n,s,r){return o.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(t,e){this.app=t},create:function(t){void 0===t.value&&(t.value=null),void 0===t.default_value&&(t.default_value=t.value);var e=null,i=this.types[t.type];return i&&"function"==typeof this[i]&&(e=this[i].call(this,t)),e||(this.app.incompatible=!0,e=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0!==t.value&&e.value(t.value),e},_fieldData:function(e){if(this.app.options.is_workflow)return e.info="Data input '"+e.name+"' ("+t.textify(e.extensions.toString())+")",e.value=null,this._fieldHidden(e);var n=this;return new i.View(this.app,{id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,data:e.options,onchange:function(){n.app.trigger("change")}})},_fieldSelect:function(t){if(0==t.options.length&&this.app.options.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];for(var n in t.options){var s=t.options[n];i.push({label:s[0],value:s[1]})}var o=e.Select;switch(t.display){case"checkboxes":o=e.Checkbox;break;case"radio":o=e.Radio}var a=this;return new o.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",optional:t.optional&&null===t.default_value,multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){a.app.trigger("change")}})},_fieldDrilldown:function(t){if(0==t.options.length&&this.app.options.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){if(a.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}}else i.value="";var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(){o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new r({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.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(4),i(18),i(11),i(7)],s=function(t,e,i,n){var s=o.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(i){this.options=t.merge(i,this.optionsDefault),this.setElement("");this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+i.title_new,tooltip:"Add new "+i.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()},_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))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(18),i(7),i(11),i(41),i(39),i(40)],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.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id;var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$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.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title,title_new:t.title,min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=t.min,l=r.size(t.cache),d=0;dd?t.cache[d]:t.inputs,e(u)}var p=new c(this.app,{label:t.title,help:t.help,field:o});this.table.add(p.$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,cls:"ui-portlet-section",operations:{button_visible:o}});a.append(s.$el),a.append(l("").addClass("ui-table-form-info").html(t.help));var r=!1;a.$content.hide(),a.$header.css("cursor","pointer"),a.$header.on("click",function(){r?(r=!1,a.$content.hide(),o.setIcon("fa-eye-slash")):(r=!0,a.$content.fadeIn("fast"),o.setIcon("fa-eye"))}),this.app.on("expand",function(t){a.$el.find("#"+t).length>0&&!r&&a.$header.trigger("click")}),t.expanded&&a.$header.trigger("click"),this.table.add(a.$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,default_value:t.default_value,collapsible:t.collapsible,collapsible_value:t.collapsible_value,help:t.help,argument:t.argument,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(31),i(16)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement(''),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$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 f in this.list)this.$el.append(this.list[f].field.$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({label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.update(n)}}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.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(11),i(7),i(42),i(38)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=t.merge(e,this.optionsDefault),Galaxy.emit.debug("form-view::initialize()","Ready to build form.",this.options);var n=parent.Galaxy;n&&n.modal?this.modal=n.modal:this.modal=new i.Modal.View,this.setElement(""),this._build()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$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)}}},_build:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();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()})},_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:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),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(35),i(46),i(5)],s=function(t,e,i){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 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Convert spaces to tabs
Use POSIX standard
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loading tool info...