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"))})),this.row_count++,i},_renderChunk:function(t){var e=this.$el.find("table");n.each(t.ck_data.split("\n"),function(t,i){""!==t&&e.append(this._renderRow(t))},this)}}),_=p.extend({initialize:function(t){p.prototype.initialize.call(this,t);var e=n.find(this.$el.parents(),function(t){return"auto"===a(t).css("overflow")});e||(e=window),this.scroll_elt=a(e)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),m=p.extend({initialize:function(t){p.prototype.initialize.call(this,t),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:t.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),g=t.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(t){var e=parent.Galaxy;if(e&&e.modal&&(this.modal=e.modal),e&&e.frame&&(this.frame=e.frame),this.modal&&this.frame){var i=t.model,n=i.get("metadata");if(i.get("file_ext")){if(this.file_ext=i.get("file_ext"),"bed"==this.file_ext){if(!(n.get("chromCol")&&n.get("startCol")&&n.get("endCol")))return void console.log("TabularButtonTrackster : Bed-file metadata incomplete.");this.col.chrom=n.get("chromCol")-1,this.col.start=n.get("startCol")-1,this.col.end=n.get("endCol")-1}if("vcf"==this.file_ext){var a=function(t,e){for(var i=0;i=200&&t<300}};s.headers={common:{Accept:"application/json, text/plain, */*"}},a.forEach(["delete","get","head"],function(t){s.headers[t]={}}),a.forEach(["post","put","patch"],function(t){s.headers[t]=a.merge(o)}),t.exports=s}).call(e,i(76))},function(t,e,i){"use strict";function n(t){for(var i in t)e.hasOwnProperty(i)||(e[i]=t[i])}Object.defineProperty(e,"__esModule",{value:!0}),n(i(18)),n(i(19)),n(i(96))},function(t,e,i){"use strict";function n(t,e,i,n){if(void 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n=t.input_list[i];if(!n||n.refresh_on_change||t.model.get("always_refresh")){var a=t.data.checksum();a!=e&&(e=a,t.model.get("onchange")())}}),this.on("reset",function(){n.each(t.element_list,function(t){t.reset()})}),this},_renderForm:function(){a(".tooltip").remove();var t=this.model.attributes;this.message=new c.default.UnescapedMessage,this.section=new h.default.View(this,{inputs:t.inputs}),this.portlet=new l.default.View({icon:t.icon,title:t.title,cls:t.cls,operations:!t.hide_operations&&t.operations,buttons:t.buttons,collapsible:t.collapsible,collapsed:t.collapsed,onchange_title:t.onchange_title}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),t.inputs&&this.$el.append(this.portlet.$el),t.message&&this.message.update({persistent:!0,status:t.status,message:t.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(2),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(r),s=i(14),l=a(s),d=i(21),c=(a(d),t.Model.extend({initialize:function(t){var e=this.get("key");this.set("id",e);var i=o.find([{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:32,hidden:!0},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label 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n=this.get(t);if(n)return n.set_value(e,i)},set_default_value:function(t,e){var i=this.get(t);if(i)return i.set("default_value",e)}},{from_models_and_saved_values:function(t,e){return e&&(t=o.map(t,function(t){return o.extend({},t,{value:e[t.key]})})),new u(t)}}),h=t.View.extend({className:"config-settings-view",render:function(){var t=this.$el;return this.collection.each(function(e,i){if(!e.get("hidden")){var a="param_"+i,r=e.get("type"),s=e.get("value"),d=n("").appendTo(t);if(d.append(n("").attr("for",a).text(e.get("label")+":")),"bool"===r)d.append(n('').attr("id",a).attr("name",a).attr("checked",s));else if("text"===r)d.append(n('').attr("id",a).val(s).click(function(){n(this).select()}));else if("select"===r){var c=n("").attr("id",a);o.each(e.get("options"),function(t){n("").text(t.label).attr("value",t.value).appendTo(c)}),c.val(s),d.append(c)}else if("color"===r){var u=n("").appendTo(d),h=n("").attr("id",a).attr("name",a).val(s).css("float","left").appendTo(u).click(function(t){n(".tooltip").removeClass("in");var e=n(this).siblings(".tooltip").addClass("in");e.css({left:n(this).position().left+n(this).width()+5,top:n(this).position().top-n(e).height()/2+n(this).height()/2}).show(),e.click(function(t){t.stopPropagation()}),n(document).bind("click.color-picker",function(){e.hide(),n(document).unbind("click.color-picker")}),t.stopPropagation()}),f=n("").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),p=n("").appendTo(u).hide(),_=n("").appendTo(p),m=(n("").appendTo(p),n.farbtastic(_,{width:100,height:100,callback:h,color:s}));u.append(n("").css("clear","both")),function(t){f.click(function(){t.setColor(l.default.get_random_color())})}(m)}else d.append(n("").attr("id",a).attr("name",a).val(s));e.help&&d.append(n("").text(e.help))}}),this},render_in_modal:function(t){var 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t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=n("")).append(this.$dropdown=n("")).append(this.$resize=n("").append(this.$resize_icon=n(""))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(e){var 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e=this.$select.select2("data");e&&(n.isArray(e)?(t=[],e.sort(function(t,e){return t.order-e.order}),a.each(e,function(e){t.push(e.id)})):t=e.id)}else t=this.$select.val();return s.default.isEmpty(t)?null:t}});e.default={View:c}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(12),d=r(l),c=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({visible:!0,data:[],id:s.default.uid(),error_text:"No options available.",wait_text:"Please 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r.inputs)if(!r.inputs[l].hidden){s=!0;break}a==n&&s?o.fadeIn("fast"):o.hide()}e.app.trigger("change")});for(var n in t.cases){var a=new v(this.app,{inputs:t.cases[n].inputs});this._append(a.$el.addClass("ui-form-section"),t.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,o=new v(i.app,{inputs:e});r.add({id:a,$el:o.$el,ondel:function(){r.del(a),i.app.trigger("change")}})}for(var i=this,n=0,r=new f.default.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=a.size(t.cache),s=0;s").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this._append(e.$el,t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=t.onchange||function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var a=new _.default(this.app,{name:t.name,label:t.hide_label?"":t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,hidden:t.hidden,fixed:t.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,t.id),n},_append:function(t,e){this.$el.append(t.addClass("section-row").attr("id",e))}});e.default={View:v}}).call(e,i(1),i(0),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(11),d=r(l),c=i(4),u=r(c),h=t.View.extend({initialize:function(t){this.list={},this.options=s.default.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new u.default.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(n("").append(this.$list=n("")).append(n("").append(this.button_new.$el)))},size:function(){return a.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var e=new u.default.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),i=new d.default.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});i.append(t.$el),i.$el.addClass("section-row").hide(),this.list[t.id]=i,this.$list.append(i.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),a.each(this.list,function(t){t.hideOperation("button_delete")}),a.isEmpty(this.list)&&this.$el.append(n("").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),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});e.default={View:h}}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.View.extend({initialize:function(e,i){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=i&&i.field||new t.View,this.model=i&&i.model||new t.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(i),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var a=this;this.$collapsible.on("click",function(){a.field.collapsed=!a.field.collapsed,e.trigger&&e.trigger("change"),a.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){a.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){i(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&-1==t.indexOf("("+e+")")&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(n.escape(this.model.get("text_value")));var a=this.model.get("error_text");if(this.$error[a?"show":"hide"](),this.$el[a?"addClass":"removeClass"]("ui-error"),this.$error_text.html(a),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var r=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+r)).attr("data-original-title",this.model.get("text_"+r)).tooltip({placement:"bottom"})}},_template:function(){return i("").addClass("ui-form-element").append(i("").addClass("ui-form-error ui-error").append(i("").addClass("fa fa-arrow-down")).append(i("").addClass("ui-form-error-text"))).append(i("").addClass("ui-form-title").append(i("").addClass("ui-form-collapsible").append(i("").addClass("ui-form-collapsible-icon")).append(i("").addClass("ui-form-collapsible-text"))).append(i("").addClass("ui-form-title-text"))).append(i("").addClass("ui-form-field").append(i("").addClass("ui-form-info")).append(i("").addClass("ui-form-backdrop"))).append(i("").addClass("ui-form-preview"))}})}).call(e,i(1),i(0),i(2))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(52),u=r(c),h=i(53),f=r(h),p=i(54),_=r(p),m=i(55),g=r(m),v=i(57),b=r(v);e.default=t.Model.extend({types:{text:"_fieldText",password:"_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",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new u.default.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var e=t.data;e||(e=[],n.each(t.options,function(t){e.push({label:t[0],value:t[1]})}));var i=d.default.Select;switch(t.display){case"checkboxes":i=d.default.Checkbox;break;case"radio":i=d.default.Radio;break;case"radiobutton":i=d.default.RadioButton}return new i.View({id:"field-"+t.id,data:e,error_text:t.error_text||"No options available",readonly:t.readonly,multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new d.default.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(t){if(t.options&&t.data)if(t.area=t.multiple,s.default.isEmpty(t.value))t.value=null;else if(a.isArray(t.value)){var e="";for(var i in t.value){if(e+=String(t.value[i]),!t.multiple)break;e+="\n"}t.value=e}return new d.default.Input({id:"field-"+t.id,type:t.type,area:t.area,readonly:t.readonly,placeholder:t.placeholder,datalist:t.datalist,onchange:t.onchange})},_fieldSlider:function(t){return new d.default.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new d.default.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new d.default.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new b.default({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new f.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new _.default.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new g.default.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new d.default.Upload({id:"field-"+t.id,onchange:t.onchange})}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n,a){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=i(3),s=r(o),l=i(4),d=r(l),c=i(22),u=r(c),h={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},f={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:h.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:h.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:h.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:h.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:h.ENABLED}]},p=t.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new t.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(n("").addClass("ui-select-content")),this.button_product=new d.default.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var a=n("").addClass("ui-form-info").append(n("").addClass("fa fa-sitemap")).append(n("").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:a.clone(),enabled:a.clone().append(n("").append(n("").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(n("").css("clear","both"))},this.$el.on("dragenter",function(t){this.lastenter=t.target,i.$el.addClass("ui-dragover")}).on("dragover",function(t){t.preventDefault()}).on("dragleave",function(t){this.lastenter===t.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(t){i._handleDrop(t)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(t){this.model.set("data",t)},value:function(t){void 0!==t&&this.model.set("value",t);var e=this.model.get("current");if(this.config[e]){var i=this.fields[e].value();if(null!==i&&(i=n.isArray(i)?i:[i],i.length>0)){var a=this._batch({values:[]});for(var r in i){var o=this.history[i[r]+"_"+this.config[e].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[r]+"'."),null;a.values.push(o)}return a.values.sort(function(t,e){return t.hid-e.hid}),a}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+t+"'.");return null},_changeCurrent:function(){var t=this;a.each(this.fields,function(e,i){t.model.get("current")==i?(e.$el.show(),a.each(t.$batch,function(e,n){e[t.config[i].batch==n?"show":"hide"]()}),t.button_type.value(i)):e.$el.hide()})},_changeType:function(){var t=this,e=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");f[e]?this.config=f[e]:(this.config=f.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+e+"'."));var i=t.model.get("data"),n=s.default.textify(this.model.get("extensions")),r=this.model.get("src_labels");this.fields=[],this.button_data=[],a.each(this.config,function(e,a){t.button_data.push({value:a,icon:e.icon,tooltip:e.tooltip}),t.fields.push(new u.default.View({optional:t.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||i&&i[e.src]&&i[e.src].length>t.model.get("pagelimit"),individual:!0,error_text:"No "+(n?n+" ":"")+(r[e.src]||"content")+" available.",onchange:function(){t.trigger("change")}}))}),this.button_type=new d.default.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){t.model.set("current",e),t.trigger("change")}}),this.$el.empty();var o=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),o=Math.max(0,36*this.fields.length)+"px"),a.each(this.fields,function(e){t.$el.append(e.$el.css({"margin-left":o}))}),a.each(this.$batch,function(e,i){t.$el.append(e.css({"margin-left":o}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var t=this;a.each(this.fields,function(e){e[t.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var t=this.model.get("data"),e=this,i={};a.each(t,function(t,n){i[n]=[],a.each(t,function(t){i[n].push({hid:t.hid,keep:t.keep,label:t.hid+": "+t.name,value:t.id,tags:t.tags}),e.history[t.id+"_"+n]=t})}),a.each(this.config,function(t,n){i[t.src]&&e.fields[n].add(i[t.src],function(t,e){return e.hid-t.hid})})},_changeValue:function(){var t=this.model.get("value");if(t&&t.values&&t.values.length>0){var e=[];a.each(t.values,function(t){e.push(t.id)});for(var i=t.values[0].src,n=t.values.length>1,r=0;rSelect Library '}});e.default={View:h}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=n(a),o=i(24),s=n(o),l=t.View.extend({initialize:function(t){var e=this;this.ftpfile_list=new s.default.View({name:"file",optional:t.optional,multiple:t.multiple,onchange:function(){t.onchange&&t.onchange(e.value())}}),this.setElement(this.ftpfile_list.$el),r.default.get({url:Galaxy.root+"api/remote_files",success:function(t){var i=[];for(var n in t)i.push({value:t[n].path,label:t[n].path});e.ftpfile_list.update(i)}})},value:function(t){return this.ftpfile_list.value(t)}});e.default={View:l}}).call(e,i(1))},function(t,e,i){"use strict";(function(t){function n(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=(n(a),i(4)),o=n(r),s=i(56),l=n(s),d=t.View.extend({initialize:function(t){var e=this;this.browse_button=new o.default.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){e.browseGenomeSpace()}}),this.filename_textbox=new o.default.Input,this.token_textbox=new o.default.Input({type:"password"}),this.setElement(this._template(t)),this.$(".ui-gs-browse-button").append(this.browse_button.$el),this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el),this.$(".ui-gs-token-textbox").append(this.token_textbox.$el)},browseGenomeSpace:function(t){var e=this;l.default.openFileBrowser({successCallback:function(t){e.value(t.destination+"^"+t.token)}})},_template:function(t){return' '},value:function(t){if(void 0===t)return this._getValue();this._setValue(t)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(t){t&&(values=t.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});e.default={View:d}}).call(e,i(1))},function(t,e,i){"use strict";Object.defineProperty(e,"__esModule",{value:!0}),e.default={openFileBrowser:function(t){var e=window.Galaxy.config.genomespace_ui_url,i=e+"upload/loadUrlToGenomespace.html?getLocation=true",n=window.open(i,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=t.successCallback,window.addEventListener("message",function(t){successCalBack(t.data)},!1),n.focus(),null!=t.errorCallback&&(n.setCallbackOnGSUploadError=config.errorCallback)}}},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return 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i={tool_id:e.model.get("id"),tool_version:e.model.get("version"),inputs:n.extend(!0,{},e.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),s.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.model.get("id")+"/build",data:i,success:function(i){e.update(i),e.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},t)),this.deferred=this.form.deferred,this.setElement(" "),this.$el.append(this.form.$el)},_customize:function(t){var e=this,i=t.model.attributes,n=new d.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),t.portlet.disable(),e.submit(i,function(){n.unwait(),t.portlet.enable()})}});i.buttons={execute:n},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},submit:function(t,e){var i=this,r={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(r))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(e&&e());if(t.action!==Galaxy.root+"tool_runner/index"){var o=n(" ").attr({action:t.action,method:t.method,enctype:t.enctype});return a.each(r.inputs,function(t,e){o.append(n(" ").attr({name:e,value:t}))}),o.hide().appendTo("body").submit().remove(),void(e&&e())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",r),s.default.request({type:"POST",url:Galaxy.root+"api/tools",data:r,success:function(t){if(e&&e(),i.$el.children().hide(),i.$el.append(i._templateSuccess(t)),t.jobs&&t.jobs.length>0){i.$el.append(n(" ",{id:"webhook-view"}));new _.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:r.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(t){e&&e(),Galaxy.emit.debug("tool-form::submit","Submission failed.",t);var n=!1;if(t&&t.err_data){var a=i.form.data.matchResponse(t.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:"Job submission failed",body:i._templateError(r,t&&t.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(t){var e=t.inputs,i=-1,n=null;for(var a in e){var r=e[a],o=this.form.data.match(a),s=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&s){if(!l.optional&&null==r)return this.form.highlight(o),!1;if(r&&r.batch){var d=r.values.length,c=d>0&&r.values[0]&&r.values[0].src;if(c)if(null===n)n=c;else if(n!==c)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===i)i=d;else if(i!==d)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+d+" selection(s) while a previous field contains "+i+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(t){if(t.jobs&&t.jobs.length>0){var e=t.jobs.length,i=1==e?"1 job has":e+" jobs have",r=n(" ").addClass("donemessagelarge").append(n(" ").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(t.outputs,function(t){r.append(n(" ").addClass("messagerow").append(n(" ").text(t.hid+": "+t.name)))}),r.append(n(" ").append(" ").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),r}return this._templateError(t,"Invalid success response. No jobs found.")},_templateError:function(t,e){return n(" ").addClass("errormessagelarge").append(n(" ").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(e||""))).append(n(" ").text(JSON.stringify(t,null,4)))}});e.default={View:m}}).call(e,i(1),i(0),i(2))},,function(t,e,i){"use strict";(function(t,i,n){Object.defineProperty(e,"__esModule",{value:!0}),e.default=t.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(t){return-1!==i.indexOf(this.attributes.async_ops,t)},add_filter:function(t,e,i){if(i){var n,a=this.attributes.filters[t];if(null===a||void 0===a)n=e;else if("string"==typeof a)if("All"==a||a==e)n=e;else{var r=[];r[0]=a,r[1]=e,n=r}else n=a,-1===n.indexOf(e)&&n.push(e);this.attributes.filters[t]=n}else this.attributes.filters[t]=e},remove_filter:function(t,e){var n=this.attributes.filters[t];if(null===n||void 0===n)return!1;if("string"==typeof n)this.attributes.filters[t]="";else{var a=i.indexOf(n,e);-1!==a&&(n[a]="")}},get_url_data:function(){var t={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(t.operation=this.attributes.operation),this.attributes.item_ids&&(t.id=this.attributes.item_ids);var e=this;return i.each(i.pairs(e.attributes.filters),function(e){t["f-"+e[0]]=e[1]}),t},get_url:function(t){return this.get("url_base")+"?"+n.param(this.get_url_data())+"&"+n.param(t)}})}).call(e,i(1),i(2),i(0))},function(t,e,i){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0});var a=i(3),r=function(t){return t&&t.__esModule?t:{default:t}}(a);e.default={grid:function(t){var e="";return e=t.embedded?this.grid_header(t)+this.grid_table(t):' '+this.grid_table(t),t.info_text&&(e+=' '+t.info_text+" "),e},grid_table:function(t){return' '},grid_header:function(t){var e='"},header:function(t){var e=" ";t.show_item_checkboxes&&(e+="| ",t.items.length>0&&(e+=''),e+=" | ");for(var i in t.columns){var n=t.columns[i];n.visible&&(e+='")}return e+=" "},body:function(e){var i="",n=0;0==e.items.length&&(i+=' | No Items | ',n=1);for(var a in e.items){var r=e.items[a],o=r.encode_id;i+=" ",e.show_item_checkboxes&&(i+=' | ');for(var s in e.columns){var l=e.columns[s];if(l.visible){var d="";l.nowrap&&(d='style="white-space:nowrap;"');var c=r.column_config[l.label],u=c.link,h=c.value,f=c.target;"string"===t.type(h)&&(h=h.replace(/\/\//g,"/"));var p="",_="";l.attach_popup&&(p="grid-"+a+"-popup",_="menubutton",""!=u&&(_+=" split"),_+=" popup"),i+="",u?(0!=e.operations.length&&(i+=' '),i+='",0!=e.operations.length&&(i+=" ")):i+='",i+=" | "}}i+=" ",n++}return i},footer:function(t){var e="";if(t.use_paging&&t.num_pages>1){var i=t.num_page_links,n=t.cur_page_num,a=t.num_pages,r=i/2,o=n-r,s=0;o<=0&&(o=1,s=r-(n-o));var l,d=r+s,c=n+d;c<=a?l=0:(c=a,l=d-(c+1-n)),0!=l&&(o-=l)<1&&(o=1),e+=' ',t.show_item_checkboxes&&(e+=" | "),e+='Page:',o>1&&(e+='1 ...');for(var u=o;u'+u+"":e+=''+u+"";c'+a+""),e+="",e+=' | Show All | '}if(t.show_item_checkboxes){e+=' | For selected items: ';for(var h in t.operations){var f=t.operations[h];f.allow_multiple&&(e+=' ')}e+=" | "}var p=!1;for(h in t.operations)if(t.operations[h].global_operation){p=!0;break}if(p){e+=' | ';for(h in t.operations){var f=t.operations[h];f.global_operation&&(e+=''+f.label+"")}e+=" | "}return t.legend&&(e+=' | '+t.legend+" | "),e},message:function(t){var e=t.status;return-1!=["success","ok"].indexOf(e)&&(e="done"),' '+n.escape(t.message)+' '},grid_filters:function(t){var e=t.default_filter_dict,i=t.filters,n="none";t.advanced_search&&(n="block");var a=!1;for(var r in t.columns){var o=t.columns[r];if("advanced"==o.filterable){var s=o.key,l=i[s],d=e[s];l&&d&&l!=d&&(n="block"),a=!0}}var c="block";"block"==n&&(c="none");var u=' ';for(var r in t.columns){var o=t.columns[r];"standard"==o.filterable&&(u+=this.grid_column_filter(t,o))}u+=" | | ",a&&(u+='Advanced Search'),u+=" |
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