diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js index 92bd429ad53..fcc295e0325 100644 --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -30,9 +30,7 @@ var LibraryDatasetView = Backbone.View.extend({ "click .btn-make-private" : "makeDatasetPrivate", "click .btn-remove-restrictions" : "removeDatasetRestrictions", "click .toolbtn_save_permissions" : "savePermissions", - "click .toolbtn_save_modifications" : "comingSoon", - // "click .btn-share-dataset" : "comingSoon" }, @@ -585,15 +583,26 @@ var LibraryDatasetView = Backbone.View.extend({ '
', '
', '', + '', - '', '<% if (item.get("can_user_modify")) { %>', - '', + '', '<% } %>', '<% if (item.get("can_user_manage")) { %>', - '/datasets/<%- item.id %>/permissions">', - // '', + '/datasets/<%- item.id %>/permissions">', + '', + '', '<% } %>', '
', @@ -613,7 +622,8 @@ var LibraryDatasetView = Backbone.View.extend({ '
', 'This dataset is unrestricted so everybody can access it. Just share the URL of this page. ', ' ', '
', '<% } %>', @@ -726,7 +736,12 @@ var LibraryDatasetView = Backbone.View.extend({ // CONTAINER START '
', '', // BREADCRUMBS @@ -838,8 +853,14 @@ var LibraryDatasetView = Backbone.View.extend({ // CONTAINER START '
', '
', - '', - '', + '', + '', '
', // BREADCRUMBS @@ -932,8 +953,18 @@ var LibraryDatasetView = Backbone.View.extend({ // CONTAINER START '
', '', // BREADCRUMBS @@ -964,30 +995,42 @@ var LibraryDatasetView = Backbone.View.extend({ '
', '

Dataset-related permissions

', '
Changes made below will affect every library item that was created from this dataset and also every history this dataset is part of.
', - '<% if (!item.get("is_unrestricted")) { %>', '

You can remove all access restrictions on this dataset. ', - '', - '

', + '', + '

', '<% } else { %>', 'This dataset is unrestricted so everybody can access it. Just share the URL of this page.', - ' ', + '', '

You can make this dataset private to you. ', - '', + '', '

', - // '

You can share this dataset privately with other Galaxy users. ', - // '', - // '

', '<% } %>', '

Roles that can access the dataset

', '
', - '
User has to have all these roles in order to access this dataset. Users without access permission cannot have other permissions on this dataset. If there are no access roles set on the dataset it is considered unrestricted.
', + '
', + 'User has to have all these roles in order to access this dataset.', + ' Users without access permission cannot have other permissions on this dataset.', + ' If there are no access roles set on the dataset it is considered unrestricted.', + '
', '

Roles that can manage permissions on the dataset

', '
', - '
User with any of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.
', - '', + '
', + 'User with any of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.', + '
', + '', '
', // CONTAINER END '
' diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map index 67b4446eea1..6d8b58c5faa 100644 --- a/static/maps/mvc/library/library-dataset-view.js.map +++ b/static/maps/mvc/library/library-dataset-view.js.map @@ -1 +1 @@ -{"version":3,"file":"library-dataset-view.js","sources":["../../../src/mvc/library/library-dataset-view.js"],"names":["define","mod_toastr","mod_library_model","mod_utils","mod_select","LibraryDatasetView","Backbone","View","extend","el","model","options","events","click .toolbtn_modify_dataset","click .toolbtn_cancel_modifications","click .toolbtn-download-dataset","click .toolbtn-import-dataset","click .toolbtn-share-dataset","click .btn-copy-link-to-clipboard","click .btn-make-private","click .btn-remove-restrictions","click .toolbtn_save_permissions","click 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t=this.model.get("status");if(this.model.get("large")?this.$el.addClass(("success"==t&&"done"||"danger"==t&&"error"||t)+"messagelarge"):this.$el.addClass("alert").addClass("alert-"+t),this.model.get("message")){if(this.$el.html(this.model.get("message")),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout),!this.model.get("persistent")){var e=this;this.timeout=window.setTimeout(function(){e.$el.fadeOut()},3e3)}}else this.$el.fadeOut();return this}}),h=o.View.extend({initialize:function(t){this.model=t&&t.model||new o.Model({type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1}).set(t),this.tagName=this.model.get("area")?"textarea":"input",this.setElement(a("<"+this.tagName+"/>")),this.listenTo(this.model,"change",this.render,this),this.render()},events:{input:"_onchange"},value:function(t){return void 0!==t&&this.model.set("value","string"==typeof t?t:""),this.model.get("value")},render:function(){return this.$el.removeClass().addClass("ui-"+this.tagName).addClass(this.model.get("cls")).attr("id",this.model.id).attr("type",this.model.get("type")).attr("placeholder",this.model.get("placeholder")).val(this.model.get("value")),this.model.get("disabled")?this.$el.attr("disabled",!0):this.$el.removeAttr("disabled"),this.$el[this.model.get("visible")?"show":"hide"](),this},_onchange:function(){this.value(this.$el.val()),this.model.get("onchange")&&this.model.get("onchange")(this.model.get("value"))}}),u=o.View.extend({initialize:function(t){this.model=t&&t.model||new o.Model(t),this.setElement(a("
").append(this.$info=a("
")).append(this.$hidden=a("
"))),this.listenTo(this.model,"change",this.render,this),this.render()},value:function(t){return void 0!==t&&this.model.set("value",t),this.model.get("value")},render:function(){return this.$el.attr("id",this.model.id),this.$hidden.val(this.model.get("value")),this.model.get("info")?this.$info.show().html(this.model.get("info")):this.$info.hide(),this}});return{Button:r.ButtonDefault,ButtonIcon:r.ButtonIcon,ButtonCheck:r.ButtonCheck,ButtonMenu:r.ButtonMenu,ButtonLink:r.ButtonLink,Input:h,Label:c,Message:d,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Select:e,Hidden:u,Slider:i,Drilldown:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({visible:!1,initialize:function(e){var i=this;this.options=t.merge(e,{id:t.uid(),title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right",collapsible:!1,collapsed:!1}),this.setElement(this._template(this.options)),this.$body=this.$(".portlet-body"),this.$title=this.$(".portlet-title-text"),this.$header=this.$(".portlet-header"),this.$content=this.$(".portlet-content"),this.$footer=this.$(".portlet-footer"),this.options.nopadding&&(this.$content.css("padding","0px"),this.$body.css("padding","0px")),this.$buttons=this.$(".portlet-buttons"),this.options.buttons?a.each(this.options.buttons,function(t,e){e.$el.prop("id",t),i.$buttons.append(e.$el)}):this.$buttons.remove(),this.$operations=this.$(".portlet-operations"),this.options.operations&&a.each(this.options.operations,function(t,e){e.$el.prop("id",t),i.$operations.append(e.$el)}),this.options.body&&this.append(this.options.body),this.collapsed=!1,this.options.collapsible&&(this.$title.addClass("no-highlight").css({cursor:"pointer","text-decoration":"underline"}),this.$title.on("click",function(){i.collapsed?i.expand():i.collapse()}),this.options.collapsed&&this.collapse())},append:function(t){this.$body.append(t)},empty:function(){this.$body.empty()},header:function(){return this.$header},body:function(){return this.$body},footer:function(){return this.$footer},show:function(){this.visible=!0,this.$el.fadeIn("fast")},hide:function(){this.visible=!1,this.$el.fadeOut("fast")},enableButton:function(t){this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(t){this.$buttons.find("#"+t).prop("disabled",!0)},hideOperation:function(t){this.$operations.find("#"+t).hide()},showOperation:function(t){this.$operations.find("#"+t).show()},setOperation:function(t,e){var i=this.$operations.find("#"+t);i.off("click"),i.on("click",e)},title:function(t){var e=this.$title;return t&&e.html(t),e.html()},collapse:function(){this.collapsed=!0,this.$content.height("0%"),this.$body.hide(),this.$footer.hide(),this.trigger("collapsed")},expand:function(){this.collapsed=!1,this.$content.height("100%"),this.$body.fadeIn("fast"),this.$footer.fadeIn("fast"),this.trigger("expanded")},disable:function(){this.$(".portlet-backdrop").show()},enable:function(){this.$(".portlet-backdrop").hide()},_template:function(t){var e='
';return t.title&&(e+='
',t.icon&&(e+=' '),e+=''+t.title+"
"),e+='
',"top"==t.placement&&(e+='
'),e+='
',"bottom"==t.placement&&(e+='
'),e+='
'}});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;n=[],s=function(){"use strict";var t={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};return t.READY_STATES=[t.OK,t.EMPTY,t.PAUSED,t.FAILED_METADATA,t.NOT_VIEWABLE,t.DISCARDED,t.ERROR],t.NOT_READY_STATES=[t.UPLOAD,t.QUEUED,t.RUNNING,t.SETTING_METADATA,t.NEW],t}.apply(e,n),!(void 0!==s&&(t.exports=s))},,function(t,e,i){var n,s;(function(o,a,r){n=[i(8),i(24),i(15)],s=function(t,e,i){var n=o.Model.extend({}),s=o.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var t=new n;a.each(a.keys(this.attributes),function(e){if(0===e.indexOf("metadata_")){var i=e.split("metadata_")[1];t.set(i,this.attributes[e]),delete this.attributes[e]}},this),this.set("metadata",t,{silent:!0})},get_metadata:function(t){return this.attributes.metadata.get(t)},urlRoot:Galaxy.root+"api/datasets"}),l=s.extend({defaults:a.extend({},s.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:!1}),initialize:function(t){s.prototype.initialize.call(this),this.attributes.chunk_index=this.attributes.first_data_chunk?1:0,this.attributes.chunk_url=Galaxy.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=Galaxy.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var t=this,e=r.Deferred();return r.getJSON(this.attributes.chunk_url,{chunk:t.attributes.chunk_index++}).success(function(i){var n;""!==i.ck_data?n=i:(t.attributes.at_eof=!0,n=null),e.resolve(n)}),e}}),c=o.Collection.extend({model:s}),d=o.View.extend({initialize:function(t){this.row_count=0,this.loading_chunk=!1,new p({model:t.model,$el:this.$el})},expand_to_container:function(){this.$el.height()").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var t=r("").attr({id:"content_table",cellpadding:0});this.$el.append(t);var e=this.model.get_metadata("column_names"),i=r("").appendTo(t),n=r("").appendTo(i);if(e)n.append("");else for(var s=1;s<=this.model.get_metadata("columns");s++)n.append("");var o=this,a=this.model.get("first_data_chunk");a?this._renderChunk(a):r.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)}),this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(t,e,i){var n=r("");e.append(t),this.row.append(e)},appendHeader:function(){this.$thead.append(this.row),this.row=a("")},add:function(t,e,i){var n=a("");e&&n.css("width",e),i&&n.css("text-align",i),n.append(t),this.row.append(n)},append:function(t,e){this._commit(t,e,!1)},prepend:function(t,e){this._commit(t,e,!0)},get:function(t){return this.$el.find("#"+t)},del:function(t){var e=this.$tbody.find("#"+t);e.length>0&&(e.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(t){this.before=this.$tbody.find(".current").attr("id"),void 0!==t&&(this.$tbody.find("tr").removeClass("current"),t&&this.$tbody.find("#"+t).addClass("current"));var e=this.$tbody.find(".current").attr("id");return void 0===e?null:(e!=this.before&&this.options.onchange&&this.options.onchange(t),e)},size:function(){return this.$tbody.find("tr").length},_commit:function(t,e,i){this.del(t),this.row.attr("id",t),i?this.$tbody.prepend(this.row):this.$tbody.append(this.row),e&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return a('')},_onclick:function(t){var e=this.value(),i=a(t.target).closest("tr").attr("id");""!=i&&i&&e!=i&&(this.options.onconfirm?this.options.onconfirm(i):this.value(i))},_ondblclick:function(t){var e=this.value();e&&this.options.ondblclick&&this.options.ondblclick(e)},_refresh:function(){0==this.row_count?this.$tmessage.show():this.$tmessage.hide()},_template:function(t){return'
"+e.join("")+""+s+"").text(t),s=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):s&&e"),n=this.model.get_metadata("columns");return this.row_count%2!==0&&i.addClass("dark_row"),e.length===n?a.each(e,function(t,e){i.append(this._renderCell(t,e))},this):e.length>n?(a.each(e.slice(0,n-1),function(t,e){i.append(this._renderCell(t,e))},this),i.append(this._renderCell(e.slice(n-1).join(" "),n-1))):n>5&&e.length===n-1?(a.each(e,function(t,e){i.append(this._renderCell(t,e))},this),i.append(r(""))):i.append(this._renderCell(t,0,n)),this.row_count++,i},_renderChunk:function(t){var e=this.$el.find("table");a.each(t.ck_data.split("\n"),function(t,i){""!==t&&e.append(this._renderRow(t))},this)}}),h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),scroll_elt=a.find(this.$el.parents(),function(t){return"auto"===r(t).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=r(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),u=d.extend({initialize:function(t){d.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.$el.innerHeight()>=this.el.scrollHeight}}),p=o.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(t){function e(t,e){for(var i=0;i';return t.icon&&(e+=' '),e+=''+t.title+""}}),i=e.extend({initialize:function(t){e.prototype.initialize.call(this,t)},_template:function(t){return''}}),n=o.View.extend({initialize:function(e){this.options=t.merge(e,{title:"Select/Unselect all",icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0}),this.setElement(this._template()),this.$title=this.$(".title"),this.$icon=this.$(".icon"),this.value(this.options.value),this.$title.html(this.options.title);var i=this;this.$el.on("click",function(){i.current=0===i.current&&2||0,i.value(i.current),i.options.onclick&&i.options.onclick()})},value:function(t,e){return void 0!==t&&(e&&0!==t&&(t=t!==e&&1||2),this.current=t,this.$icon.removeClass().addClass("icon").addClass(this.options.icons[t]),this.options.onchange&&this.options.onchange(t)),this.current},_template:function(){return'
'}}),s=o.View.extend({initialize:function(e){this.options=t.merge(e,{id:t.uid(),title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null}),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var i=this;a(this.el).on("click",function(){a(".tooltip").hide(),e.onclick&&!i.disabled&&e.onclick()}),this.$button.tooltip({title:e.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(t){this.$("i").removeClass(this.options.icon).addClass(t),this.options.icon=t},_template:function(t){var e="";t.title&&(e="width: auto;");var i='
';return i+=t.title?' '+t.title+"":'',i+="
"}}),r=o.View.extend({$menu:null,initialize:function(e){this.options=t.merge(e,{id:"",title:"",floating:"right",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}),this.setElement(a(this._template(this.options)));var i=a(this.el).find(".root"),n=this;i.on("click",function(t){a(".tooltip").hide(),t.preventDefault(),n.options.onclick&&n.options.onclick()}),this.options.visible||this.hide(),i.tooltip({title:e.tooltip,placement:"bottom"})},show:function(){a(this.el).show()},hide:function(){a(this.el).hide()},addMenu:function(e){var i={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};i=t.merge(e,i),this.$menu||(a(this.el).append(this._templateMenu()),this.$menu=a(this.el).find(".menu"));var n=a(this._templateMenuItem(i));n.on("click",function(t){i.onclick&&(t.preventDefault(),i.onclick())}),this.$menu.append(n),i.divider&&this.$menu.append(a(this._templateDivider()))},_templateMenuItem:function(t){var e='
  • '),e+=" "+t.title+"
    • "},_templateMenu:function(){return'
    '+t.content+"
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    "},requirements:function(t){var e="This tool requires ";for(var i in t.requirements){var n=t.requirements[i];e+=n.name,n.version&&(e+=" (Version "+n.version+")"),ihere for more information.'}}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(9),i(7)],s=function(t,e,i){var n=o.View.extend({initialize:function(t){var n=this;this.options=t,this.name=t.name||"element",this.multiple=t.multiple||!1,this.message=new i.Message,this.portlet=new e.View({cls:"ui-portlet-section"}),this.select=new i.Select.View({optional:t.optional}),this.button=new i.ButtonIcon({icon:"fa fa-sign-in",floating:"left",tooltip:"Insert new "+this.name,onclick:function(){n.add({id:n.select.value(),name:n.select.text()})}}),this.setElement(this._template(t)),this.$(".ui-list-message").append(this.message.$el),this.$(".ui-list-portlet").append(this.portlet.$el),this.$(".ui-list-button").append(this.button.$el),this.$(".ui-list-select").append(this.select.$el)},value:function(t){if(void 0!==t){if(this.portlet.empty(),a.isArray(t))for(var e in t){var i=t[e],n=null,s=null;"string"!=a.type(i)?(n=i.id,s=i.name):n=s=i,null!=n&&this.add({id:n,name:s})}this._refresh()}var o=[];return this.$(".ui-list-id").each(function(){o.push({id:a(this).prop("id"),name:a(this).find(".ui-list-name").html()})}),0==o.length?null:o},add:function(e){var i=this;if(0===this.$('[id="'+e.id+'"]').length)if(t.validate(e.id)){var n=a(this._templateRow({id:e.id,name:e.name}));n.on("click",function(){n.remove(),i._refresh()}),n.on("mouseover",function(){n.addClass("portlet-highlight")}),n.on("mouseout",function(){n.removeClass("portlet-highlight")}),this.portlet.append(n),this._refresh()}else this.message.update({message:"Please select a valid "+this.name+".",status:"danger"});else this.message.update({message:"This "+this.name+" is already in the list."})},update:function(t){this.select.update(t)},_refresh:function(){this.$(".ui-list-id").length>0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(t){return'
    '},_templateRow:function(t){return'
    '+t.name+"
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    '),this.$message=a("
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this.ERRORS_},this.parse=function(t){for(var e=0;en;n++){var l=i[n],c=!1;"\\"==l&&a-1>n?l=i[++n]:"{"!=l&&"}"!=l||(c=!0),c||(r+=l)}t.Fields[e]=r}if("string"==t.ObjectType)for(var e in t.Fields)this.MACROS_[e]=t.Fields[e];else this.CALLBACK_(t)},this.processCharacter_=function(t){if(this.CHAR_++,this.CHAR_IN_LINE_++,"\n"==t&&(this.LINE_++,this.CHAR_IN_LINE_=1),this.SKIPTILLEOL_)return void("\n"==t&&(this.SKIPTILLEOL_=!1));if(this.SKIPCOMMENT_&&"%"==t)return void(this.SKIPTILLEOL_=!0);if(!this.SKIPWS_||!/\s/.test(t)){this.SKIPWS_=!1,this.SKIPCOMMENT_=!1,this.SKIPTILLEOL_=!1;for(var e=!0;e;)switch(e=!1,this.STATE_){case this.STATES_.ENTRY_OR_JUNK:"@"==t&&(this.STATE_=this.STATES_.OBJECT_TYPE,this.DATA_={ObjectType:""}),this.BRACETYPE_=null,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(t))this.DATA_.ObjectType+=t.toLowerCase(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;else{var i=this.DATA_.ObjectType;"comment"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:"string"==i?(this.DATA_.ObjectType=i,this.DATA_.Fields={},this.BRACETYPE_=t,this.BRACECOUNT_=1,this.STATE_=this.STATES_.KV_KEY,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={Key:""}):"preamble"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:i in this.ENTRY_TYPES_?(this.DATA_.ObjectType="entry",this.DATA_.EntryType=i,this.DATA_.EntryKey="",this.STATE_=this.STATES_.ENTRY_KEY,e=!0):(this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"'),this.STATE_=this.STATES_.ENTRY_OR_JUNK)}break;case this.STATES_.ENTRY_KEY:if(("{"===t||"("===t)&&null==this.BRACETYPE_){this.BRACETYPE_=t,this.BRACECOUNT_=1,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break}/[,%\s]/.test(t)?this.DATA_.EntryKey.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):null==this.BRACETYPE_?(this.error_("No opening brace for 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this.MACROS_?this.PARSETMP_.Value=this.MACROS_[a]:this.error_("Reference to an undefined macro: "+a),e=!0,o=!0}else 0!=s.length&&"\\"==s[s.length-1]||n["{"].length>0&&(n["{"].splice(n["{"].length-1,1),0==n["{"].length+n['"'].length&&(o=!0))}o?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.KV_KEY,this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value,this.PARSETMP_={Key:""},this.VALBRACES_=null):this.PARSETMP_.Value+=t}}},this.CHARCONV_=[[/\\space /g," "],[/\\textdollar /g,"$"],[/\\textquotesingle /g,"'"],[/\\ast /g,"*"],[/\\textbackslash /g,"\\"],[/\\\^\{\}/g,"^"],[/\\textasciigrave /g,"`"],[/\\lbrace /g,"{"],[/\\vert /g,"|"],[/\\rbrace /g,"}"],[/\\textasciitilde /g,"~"],[/\\textexclamdown /g,"¡"],[/\\textcent /g,"¢"],[/\\textsterling /g,"£"],[/\\textcurrency /g,"¤"],[/\\textyen /g,"¥"],[/\\textbrokenbar /g,"¦"],[/\\textsection /g,"§"],[/\\textasciidieresis /g,"¨"],[/\\textcopyright /g,"©"],[/\\textordfeminine /g,"ª"],[/\\guillemotleft /g,"«"],[/\\lnot 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this.ERRORS_},this.parse=function(t){for(var e=0;en;n++){var l=i[n],c=!1;"\\"==l&&a-1>n?l=i[++n]:("{"==l||"}"==l)&&(c=!0),c||(r+=l)}t.Fields[e]=r}if("string"==t.ObjectType)for(var e in t.Fields)this.MACROS_[e]=t.Fields[e];else this.CALLBACK_(t)},this.processCharacter_=function(t){if(this.CHAR_++,this.CHAR_IN_LINE_++,"\n"==t&&(this.LINE_++,this.CHAR_IN_LINE_=1),this.SKIPTILLEOL_)return void("\n"==t&&(this.SKIPTILLEOL_=!1));if(this.SKIPCOMMENT_&&"%"==t)return void(this.SKIPTILLEOL_=!0);if(!this.SKIPWS_||!/\s/.test(t)){this.SKIPWS_=!1,this.SKIPCOMMENT_=!1,this.SKIPTILLEOL_=!1;for(var e=!0;e;)switch(e=!1,this.STATE_){case this.STATES_.ENTRY_OR_JUNK:"@"==t&&(this.STATE_=this.STATES_.OBJECT_TYPE,this.DATA_={ObjectType:""}),this.BRACETYPE_=null,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(t))this.DATA_.ObjectType+=t.toLowerCase(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;else{var i=this.DATA_.ObjectType;"comment"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:"string"==i?(this.DATA_.ObjectType=i,this.DATA_.Fields={},this.BRACETYPE_=t,this.BRACECOUNT_=1,this.STATE_=this.STATES_.KV_KEY,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={Key:""}):"preamble"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:i in this.ENTRY_TYPES_?(this.DATA_.ObjectType="entry",this.DATA_.EntryType=i,this.DATA_.EntryKey="",this.STATE_=this.STATES_.ENTRY_KEY,e=!0):(this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"'),this.STATE_=this.STATES_.ENTRY_OR_JUNK)}break;case this.STATES_.ENTRY_KEY:if(("{"===t||"("===t)&&null==this.BRACETYPE_){this.BRACETYPE_=t,this.BRACECOUNT_=1,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break}/[,%\s]/.test(t)?this.DATA_.EntryKey.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):null==this.BRACETYPE_?(this.error_("No opening brace for 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    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
    ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);-1!=g&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var a=0;for(var f in h)e(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='
    ';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
    '+t.label+"
    ",e+='
    ',e+='
    ',t.help&&(e+=t.help),t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")"),e+='
    ',t.collapsible_preview&&(e+='
    '+t.text_value+"
    "),e+="
    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(39),i(53),i(52),i(49)],s=function(t,e,i,n,s,l){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){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(this.app.incompatible=!0,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){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];a.each(t.options,function(t){i.push({label:t[0],value:t[1]})});var n=e.Select;switch(t.display){case"checkboxes":n=e.Checkbox;break;case"radio":n=e.Radio}var s=this;return new n.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){s.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.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(r.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=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,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 l({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(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),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'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});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(10),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('
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    "].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 ){ %>",'
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    ',"<% } %>","<% } %>","
    "],"dataset"),o=n.wrapTemplate(['
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    ',s("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),a={};a[e.OK]=a[e.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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    ","<% } %>","<% if( dataset.file_ext ){ %>",'
    ','",'<%- dataset.file_ext %>',"
    ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
    ','",'',"<%- 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(['
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    '],"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 ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);-1!=g&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var a=0;for(var f in h)e(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext: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(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),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),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='
    ';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
    '+t.label+"
    ",e+='
    ',e+='
    ',t.help&&(e+=t.help),t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")"),e+='
    ',t.collapsible_preview&&(e+='
    '+t.text_value+"
    "),e+="
    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(39),i(53),i(52),i(49)],s=function(t,e,i,n,s,l){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){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(this.app.incompatible=!0,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){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];a.each(t.options,function(t){i.push({label:t[0],value:t[1]})});var n=e.Select;switch(t.display){case"checkboxes":n=e.Checkbox;break;case"radio":n=e.Radio}var s=this;return new n.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){s.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.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(r.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=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,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 l({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(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),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.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$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(10),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(10),i(6),i(5)],s=function(t,e,i,n,s,l){"use strict";var c="history",d=o.Collection.extend(s.LoggableMixin).extend({_logNamespace:c,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(){function t(t){return!t.inReadyState()}return new d(this.filter(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 d(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new d(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new d(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new d(this.filter(t))},visibleAndUndeleted:function(){function t(t){return t.get("visible")&&!t.get("deleted")}return new d(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetch:function(t){return t=t||{},t.data=a.defaults(t.data||{},{v:"dev"}),o.Collection.prototype.fetch.call(this,t)},fetchUpdated:function(t,e){return e=e||{},e.traditional=!0,e.data=[{name:"v",value:"dev"}],t&&(e.data=e.data.concat(this._filtersFromMap({"update_time-ge":t.toISOString()}))),e.merge=!0,e.remove=!1,this.fetch(e)},_filtersFromMap:function(t){var e=[];return a.each(t,function(t,i){e.push({name:"q",value:i}),e.push({name:"qv",value:t})}),e},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:d}}.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 %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),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.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){return t=t.tool_model||t,t.display?(a._buildForm(t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),void e.resolve()):void(window.location=Galaxy.root)},error:function(t,n){var s=t&&t.err_msg||"Uncaught error.";401==n.status?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+a.options.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:s,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(12),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.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new w({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof f){var n=new b({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new w({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof f){var s=new b({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:t.template(['',' ',''].join("")),panel_section:t.template(['
    ','<%- name %>',"
    ",'