diff --git a/static/scripts/mvc/upload/upload-ftp.js b/static/scripts/mvc/upload/upload-ftp.js
index 62bf8584238..7a1242d9d3b 100644
--- a/static/scripts/mvc/upload/upload-ftp.js
+++ b/static/scripts/mvc/upload/upload-ftp.js
@@ -35,6 +35,7 @@ return Backbone.View.extend({
     
     // fill table
     _fill: function(ftp_files) {
+        var self = this;
         if (ftp_files && ftp_files.length > 0) {
             // add table
             this.$el.find('#upload-ftp-content').html($(this._templateTable()));
@@ -49,11 +50,43 @@ return Backbone.View.extend({
             // update stats
             this.$el.find('#upload-ftp-number').html(ftp_files.length + ' files');
             this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true));
+
+            var selectAll = this.$el.find('#selectAll');
+
+            // call method to determine and set selectAll status on loading
+            this._updateSelectAll(selectAll);
+
+            // selectAll checkbox has been clicked
+            selectAll.on('click', function() {
+                var checkboxes=$(this).parents().find('tr.upload-ftp-row>td>div');
+                var len = checkboxes.length;
+                $this = $(this);
+                var allChecked = !($this.hasClass('fa-check-square-o'));
+
+                // change state of the sub-checkboxes
+                for(i = 0; i < len; i++) {
+                    if(allChecked) {
+                        // all checkboxes should be checked
+                        if(checkboxes.eq(i).hasClass('fa-square-o')) {
+                            // if they are not checked, check them
+                            checkboxes.eq(i).trigger('updateUpBox');
+                        }
+                    } else {
+                        // no checkboxes should be checked
+                        if(checkboxes.eq(i).hasClass('fa-check-square-o')) {
+                            // if they are checked, uncheck them
+                            checkboxes.eq(i).trigger('updateUpBox');
+                        }
+                    }
+                }
+
+                self._updateSelectAll(selectAll);
+            });
         } else {
             // add info
             this.$el.find('#upload-ftp-content').html($(this._templateInfo()));
         }
-        
+
         // hide spinner
         this.$el.find('#upload-ftp-wait').hide();
     },
@@ -79,18 +112,18 @@ return Backbone.View.extend({
         } else {
             icon_class = this.options.class_add;
         }
-        
+
         // add icon class
         $icon.addClass(icon_class);
-
-        // click to add ftp files
-        $it.on('click', function() {
+        
+        // add files to the uploadbox
+        $it.on('updateUpBox', function() {
             // find model
             var model_index = self._find(ftp_file);
-            
+
             // update icon
             $icon.removeClass();
-                
+
             // add model
             if (!model_index) {
                 // add to uploadbox
@@ -100,19 +133,55 @@ return Backbone.View.extend({
                     size        : ftp_file.size,
                     path        : ftp_file.path
                 }]);
-                
+
                 // add new icon class
                 $icon.addClass(self.options.class_remove);
             } else {
                 // remove
                 self.app.collection.remove(model_index);
-                
+
                 // add new icon class
                 $icon.addClass(self.options.class_add);
             }
         });
+
+        // click to add ftp files
+        $it.on('click', function() {
+            //trigger my new event
+            $icon.trigger('updateUpBox');
+
+            // click to add ftp files
+            // modify selectAll box based on number of checkboxes checked
+            var selectBox=$icon.parents().find('#selectAll');
+            // determine and set state of selectAll after sub-checkbox clicked
+            self._updateSelectAll(selectBox);
+        });
     },
-    
+
+    _updateSelectAll: function(selectBox) {
+        // array of all checkboxes
+        var checkboxes=selectBox.parents().find('tr.upload-ftp-row>td>div');
+        // array of only checked checkboxes
+        var checkedCheckboxes=selectBox.parents().find('tr.upload-ftp-row>td>div.fa-check-square-o');
+        var lenAll = checkboxes.length;
+        var lenChecked = checkedCheckboxes.length;
+
+        // determine which state the selectAll checkbox needs to be and setting it
+        if(lenChecked > 0 && lenChecked !== lenAll) {
+            // indeterminate state
+            selectBox.removeClass('fa-square-o fa-check-square-o');
+            selectBox.addClass('fa-minus-square-o');
+        } else if(lenChecked === lenAll) {
+            // checked state
+            selectBox.removeClass('fa-square-o fa-minus-square-o');
+            selectBox.addClass('fa-check-square-o');
+        } else if(lenChecked === 0) {
+            // unchecked state
+            selectBox.removeClass('fa-check-square-o fa-minus-square-o');
+            selectBox.addClass('fa-square-o');
+        }
+    },
+
     // get model index
     _find: function(ftp_file) {
         // check if exists already
@@ -149,7 +218,7 @@ return Backbone.View.extend({
                 '<table class="grid" style="float: left;">' +
                     '<thead>' +
                         '<tr>' +
-                            '<th></th>' +
+                            '<th><div id="selectAll" class="upload-icon-button fa fa-square-o" ></th>' +
                             '<th>Name</th>' +
                             '<th>Size</th>' +
                             '<th>Created</th>' +
diff --git a/static/scripts/mvc/upload/upload-model.js b/static/scripts/mvc/upload/upload-model.js
index 0acf8a36c2e..6d1757e3582 100644
--- a/static/scripts/mvc/upload/upload-model.js
+++ b/static/scripts/mvc/upload/upload-model.js
@@ -14,6 +14,7 @@ var Model = Backbone.Model.extend({
         file_type       : null,
         file_path       : '',
         percentage      : 0,
+        row             : null,
         
         // settings
         space_to_tabs   : false,
diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js
index d7f9c385e80..ce40eb8ac12 100644
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -42,6 +42,9 @@ return Backbone.View.extend({
         // link app
         this.app = app;
         
+        // default value for extension of files
+        var default_ext = 'Auto-detect';
+
         // link this
         var self = this;
         
@@ -75,15 +78,28 @@ return Backbone.View.extend({
         // initialize genome
         this.model.set('genome', self.select_genome.value());
 
+        // ensure files added after an individual row has changed 
+        // default to Auto-detect instead of ---
+        if(!(this.app.select_extension.value() === '---')){
+            this.default_ext = this.app.select_extension.value();
+        }
+
         // select extension
         this.select_extension = new Select.View({
             css: 'extension',
             onchange : function() {
                 self.model.set('extension', self.select_extension.value());
+                // if user has changed individual row type, then change "set all" 
+                // type to '---'
+                if(!(self.select_extension.value() === app.select_extension.value()))
+                {
+                    var newExte = '---';
+                    app.select_extension.value(newExte);
+                }
             },
             data: self.app.list_extensions,
             container: it.find('#extension'),
-            value: self.model.get('extension')
+            value: self.default_ext
         });
         
         // initialize extension
@@ -139,6 +155,7 @@ return Backbone.View.extend({
         this.app.collection.on('reset', function() {
             self.remove();
         });
+        self.model.set('row', self);
     },
     
     // render
diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js
index bbec3bdad75..3aead73b2aa 100644
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -6,6 +6,7 @@ define(["utils/utils",
         "mvc/upload/upload-ftp",
         "mvc/ui/ui-popover",
         "mvc/ui/ui-modal",
+        "mvc/ui/ui-select",
         "utils/uploadbox"],
        
         function(   Utils,
@@ -14,7 +15,8 @@ define(["utils/utils",
                     UploadItem,
                     UploadFtp,
                     Popover,
-                    Modal
+                    Modal,
+                    Select
                 ) {
 
 // galaxy upload
@@ -35,6 +37,9 @@ return Backbone.View.extend({
     
     // current history
     current_history: null,
+
+    // extension selector
+    select_extension : null,
     
     // current upload size
     upload_size: 0,
@@ -119,11 +124,19 @@ return Backbone.View.extend({
                         description_url : datatypes[key].description_url
                     });
                 }
-                
+
                 // sort
                 self.list_extensions.sort(function(a, b) {
                     return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
                 });
+
+                // add the '---' extension for use when the row types are changed individually
+                self.list_extensions.push({
+                        id              : "---",
+                        text            : "---",
+                        description     : "",
+                        description_url : ""
+                    });
                 
                 // add auto field
                 if (!self.options.datatypes_disable_auto) {
@@ -218,6 +231,29 @@ return Backbone.View.extend({
                 title       : 'FTP files',
                 container   : button
             });
+
+             // select extension
+            this.select_extension = new Select.View({
+                css: 'extension',
+                onchange : function() {
+                    var newExten = self.select_extension.value()
+                    var len = self.collection.models.length;
+                    // Only trigger changing the rows if the "set all" isn't set to '---' 
+                    // Prevents recursively changing the rows after an individual row has been changed
+                    if(!(newExten === '---')){
+                        for(i = 0; i < len; i++){
+                            self.collection.models[i].attributes['row'].select_extension.value(newExten);
+                        }
+                    }
+                },
+                data: self.list_extensions,
+                container: self.$el.parents().find('#extension'),
+                value: self.list_extensions[0]
+            });
+
+            // handle extension info popover
+            self.$el.parents().find('#extension-info_out').on('click' , function(e) { self._showExtensionInfo(); })
+                                                          .on('mousedown', function(e) { e.preventDefault(); });
         }
         
         // show modal
@@ -230,6 +266,60 @@ return Backbone.View.extend({
         this._updateScreen();
     },
 
+    _showExtensionInfo : function() {
+        // initialize
+        var self = this;
+        var $el = $(this.el).parents().find('#extension-info_out');
+        var extension = self.select_extension.value();
+  
+        var title = this.select_extension.text();
+
+        var description = _.findWhere(self.list_extensions, {'id': extension});
+
+        // create popup
+        if (!this.extension_popup) {
+            this.extension_popup = new Popover.View({
+                placement: 'bottom',
+                container: $el
+            });
+        }
+
+        // show / hide popup
+        if (!this.extension_popup.visible) {
+            this.extension_popup.title(title);
+            this.extension_popup.empty();
+            this.extension_popup.append(this._templateDescription(description));
+            this.extension_popup.show();
+        } else {
+            this.extension_popup.hide();
+        }
+    },
+
+    _showSettings : function() {
+        // check if popover is visible
+        if (!this.settings.visible) {
+            // show popover
+            this.settings.empty();
+            this.settings.append((new UploadSettings(this)).$el);
+            this.settings.show();
+        } else {
+            // hide popover
+            this.settings.hide();
+        }
+    },
+
+    _templateDescription: function(options) {
+        if (options.description) {
+            var tmpl = options.description;
+            if (options.description_url) {
+                tmpl += '&nbsp;(<a href="' + options.description_url + '" target="_blank">read more</a>)';
+            }
+            return tmpl;
+        } else {
+            return 'There is no description available for this file extension.';
+        }
+    },
+
     //
     // events triggered by collection
     //
@@ -513,6 +603,9 @@ return Backbone.View.extend({
             
             // remove from queue
             this.uploadbox.reset();
+
+            // reset value for universal type drop-down
+            this.select_extension.value(this.list_extensions[0]);
             
             // reset button
             this.ui_button.set('percentage', 0);
@@ -606,7 +699,12 @@ return Backbone.View.extend({
 
     // load html template
     _template: function(id, idInfo) {
-        return  '<div id="' + id + '" class="upload-box">' +
+        return '<div id="uploadhead" class="uploadhead">' +
+                    '<span class="fftext">"Set All" Types:&nbsp;&nbsp</span>' +
+                    '<span id="extension" class="extension"/>&nbsp;&nbsp' +
+                    '<span id="extension-info_out" class="upload-icon-button fa fa-search"/> ' +
+                '</div>' +
+                '<div id="' + id + '" class="upload-box">' +
                     '<table id="upload-table" class="table table-striped" style="display: none;">' +
                         '<thead>' +
                             '<tr>' +
@@ -622,7 +720,9 @@ return Backbone.View.extend({
                         '<tbody></tbody>' +
                     '</table>' +
                 '</div>' +
-                '<h6 id="' + idInfo + '" class="upload-info"></h6>';
+                '<div class="uploadfoot">' +
+                    '<h6 id="' + idInfo + '" class="upload-info"></h6>' +
+                '</div>' ;
     }
 });
 
diff --git a/static/scripts/packed/mvc/upload/upload-ftp.js b/static/scripts/packed/mvc/upload/upload-ftp.js
index 0d5d1c4e195..35cc837e891 100644
--- a/static/scripts/packed/mvc/upload/upload-ftp.js
+++ b/static/scripts/packed/mvc/upload/upload-ftp.js
@@ -1 +1 @@
-define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c&&c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})});
\ No newline at end of file
+define(["utils/utils"],function(e){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(t){this.app=t;var n=this;this.setElement(this._template()),e.get({url:galaxy_config.root+"api/ftp_files",success:function(e){n._fill(e)},error:function(){n._fill()}})},events:{mousedown:function(e){e.preventDefault()}},_fill:function(t){var n=this;if(t&&t.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var r=0;for(key in t)this.add(t[key]),r+=t[key].size;this.$el.find("#upload-ftp-number").html(t.length+" files"),this.$el.find("#upload-ftp-disk").html(e.bytesToString(r,!0));var s=this.$el.find("#selectAll");this._updateSelectAll(s),s.on("click",function(){var e=$(this).parents().find("tr.upload-ftp-row>td>div"),t=e.length;$this=$(this);var r=!$this.hasClass("fa-check-square-o");for(i=0;i<t;i++)r?e.eq(i).hasClass("fa-square-o")&&e.eq(i).trigger("updateUpBox"):e.eq(i).hasClass("fa-check-square-o")&&e.eq(i).trigger("updateUpBox");n._updateSelectAll(s)})}else this.$el.find("#upload-ftp-content").html($(this._templateInfo()));this.$el.find("#upload-ftp-wait").hide()},add:function(e){var t=this,n=$(this._templateRow(e)),r=n.find(".icon");$(this.el).find("tbody").append(n);var i="";this._find(e)?i=this.options.class_remove:i=this.options.class_add,r.addClass(i),n.on("updateUpBox",function(){var n=t._find(e);r.removeClass(),n?(t.app.collection.remove(n),r.addClass(t.options.class_add)):(t.app.uploadbox.add([{mode:"ftp",name:e.path,size:e.size,path:e.path}]),r.addClass(t.options.class_remove))}),n.on("click",function(){r.trigger("updateUpBox");var e=r.parents().find("#selectAll");t._updateSelectAll(e)})},_updateSelectAll:function(e){var t=e.parents().find("tr.upload-ftp-row>td>div"),n=e.parents().find("tr.upload-ftp-row>td>div.fa-check-square-o"),r=t.length,i=n.length;i>0&&i!==r?(e.removeClass("fa-square-o fa-check-square-o"),e.addClass("fa-minus-square-o")):i===r?(e.removeClass("fa-square-o fa-minus-square-o"),e.addClass("fa-check-square-o")):i===0&&(e.removeClass("fa-check-square-o fa-minus-square-o"),e.addClass("fa-square-o"))},_find:function(e){var t=this.app.collection.where({file_path:e.path}),n=null;for(var r in t){var i=t[r];i.get("status")=="init"&&i.get("file_mode")=="ftp"&&(n=i.get("id"))}return n},_templateRow:function(t){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+t.path+"</p></td>"+'<td style="white-space: nowrap;">'+e.bytesToString(t.size)+"</td>"+'<td style="white-space: nowrap;">'+t.ctime+"</td>"+"</tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th><div id="selectAll" class="upload-icon-button fa fa-square-o" ></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+"</strong> using your Galaxy credentials (email address and password).</div>"+'<div id="upload-ftp-content"></div>'+"<div>"}})});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/upload/upload-model.js b/static/scripts/packed/mvc/upload/upload-model.js
index d8fed66cbed..ebbc0df4f84 100644
--- a/static/scripts/packed/mvc/upload/upload-model.js
+++ b/static/scripts/packed/mvc/upload/upload-model.js
@@ -1 +1 @@
-define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",percentage:0,space_to_tabs:false,to_posix_lines:true}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}});
\ No newline at end of file
+define([],function(){var e=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",percentage:0,row:null,space_to_tabs:!1,to_posix_lines:!0}}),t=Backbone.Collection.extend({model:e});return{Model:e,Collection:t}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/upload/upload-row.js b/static/scripts/packed/mvc/upload/upload-row.js
index d15cd9feea9..673b66ebc47 100644
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1 +1 @@
-define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.model.set("genome",f.select_genome.value());this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});this.model.set("extension",f.select_extension.value());h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=_.findWhere(this.app.list_extensions,{id:i});if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+='&nbsp;(<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/>&nbsp;&nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(e,t,n,r,i){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(e,n){this.app=e;var s="Auto-detect",o=this;this.model=new t.Model(n),this.setElement(this._template(n));var u=this.$el;this.settings=new r.View({title:"Upload configuration",container:u.find("#settings"),placement:"bottom"}),this.select_genome=new i.View({css:"genome",onchange:function(){o.model.set("genome",o.select_genome.value())},data:o.app.list_genomes,container:u.find("#genome"),value:o.model.get("genome")}),this.model.set("genome",o.select_genome.value()),this.app.select_extension.value()!=="---"&&(this.default_ext=this.app.select_extension.value()),this.select_extension=new i.View({css:"extension",onchange:function(){o.model.set("extension",o.select_extension.value());if(o.select_extension.value()!==e.select_extension.value()){var t="---";e.select_extension.value(t)}},data:o.app.list_extensions,container:u.find("#extension"),value:o.default_ext}),this.model.set("extension",o.select_extension.value()),u.find("#symbol").on("click",function(){o._removeRow()}),u.find("#extension-info").on("click",function(e){o._showExtensionInfo()}).on("mousedown",function(e){e.preventDefault()}),u.find("#settings").on("click",function(e){o._showSettings()}).on("mousedown",function(e){e.preventDefault()}),u.find("#text-content").on("keyup",function(e){o.model.set("url_paste",$(e.target).val()),o.model.set("file_size",$(e.target).val().length)}),u.find("#space_to_tabs").on("change",function(e){o.model.set("space_to_tabs",$(e.target).prop("checked"))}),this.model.on("change:percentage",function(){o._refreshPercentage()}),this.model.on("change:status",function(){o._refreshStatus()}),this.model.on("change:info",function(){o._refreshInfo()}),this.model.on("change:genome",function(){o._refreshGenome()}),this.model.on("change:file_size",function(){o._refreshFileSize()}),this.model.on("remove",function(){o.remove()}),this.app.collection.on("reset",function(){o.remove()}),o.model.set("row",o)},render:function(){var t=this.model.get("file_name"),n=this.model.get("file_size"),r=this.model.get("file_mode"),i=this.$el;i.find("#title").html(t),i.find("#size").html(e.bytesToString(n)),i.find("#mode").removeClass().addClass("mode");if(r=="new"){var s=i.find("#text"),o=this.options.padding,u=i.width()-2*o,a=i.height()-o;s.css("width",u+"px"),s.css("top",a+"px"),i.height(a+s.height()+2*o),s.show(),i.find("#mode").addClass("fa fa-pencil")}r=="local"&&i.find("#mode").addClass("fa fa-laptop"),r=="ftp"&&i.find("#mode").addClass("fa fa-code-fork")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var e=this.model.get("genome");this.select_genome.value(e)},_refreshInfo:function(){var e=this.model.get("info");e?this.$el.find("#info").html("<strong>Failed: </strong>"+e).show():this.$el.find("#info").hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:e+"%"}),e!=100?this.$el.find("#percentage").html(e+"%"):this.$el.find("#percentage").html("Adding to history...")},_refreshStatus:function(){var e=this.$el,t=this.model.get("status"),n=this.status_classes[t],r=this.$el.find("#symbol");r.removeClass(),r.addClass(n),t=="init"?(this.select_genome.enable(),this.select_extension.enable(),e.find("#text-content").attr("disabled",!1),e.find("#space_to_tabs").attr("disabled",!1)):(this.select_genome.disable(),this.select_extension.disable(),e.find("#text-content").attr("disabled",!0),e.find("#space_to_tabs").attr("disabled",!0)),t=="success"&&(e.addClass("success"),e.find("#percentage").html("100%")),t=="error"&&(e.addClass("danger"),e.find(".progress").remove())},_refreshFileSize:function(){var t=this.model.get("file_size");this.$el.find("#size").html(e.bytesToString(t))},_removeRow:function(){var e=this.model.get("status");(e=="init"||e=="success"||e=="error")&&this.app.collection.remove(this.model)},_showExtensionInfo:function(){var e=$(this.el).find("#extension-info"),t=this.model.get("extension"),n=this.select_extension.text(),i=_.findWhere(this.app.list_extensions,{id:t});this.extension_popup||(this.extension_popup=new r.View({placement:"bottom",container:e})),this.extension_popup.visible?this.extension_popup.hide():(this.extension_popup.title(n),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(i)),this.extension_popup.show())},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append((new n(this)).$el),this.settings.show())},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."},_template:function(e){return'<tr id="upload-item-'+e.id+'" class="upload-item">'+"<td>"+'<div style="position: relative;">'+'<div id="mode"></div>'+'<div id="title" class="title"></div>'+'<div id="text" class="text">'+'<div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div>'+'<textarea id="text-content" class="text-content form-control"></textarea>'+"</div>"+"</div>"+"</td>"+"<td>"+'<div id="size" class="size"></div>'+"</td>"+"<td>"+'<div id="extension" class="extension" style="float: left;"/>&nbsp;&nbsp'+'<div id="extension-info" class="upload-icon-button fa fa-search"/>'+"</td>"+"<td>"+'<div id="genome" class="genome" />'+"</td>"+'<td><div id="settings" class="upload-icon-button fa fa-gear"></div>'+"<td>"+'<div id="info" class="info">'+'<div class="progress">'+'<div class="progress-bar progress-bar-success"></div>'+'<div id="percentage" class="percentage">0%</div>'+"</div>"+"</div>"+"</td>"+"<td>"+'<div id="symbol" class="'+this.status_classes.init+'"></div>'+"</td>"+"</tr>"}})});
\ No newline at end of file
diff --git a/static/style/blue/base.css b/static/style/blue/base.css
index 9164ff5a0e0..2f74cba6450 100644
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -119,6 +119,12 @@ th{text-align:left}
 .table caption+thead tr:first-child th,.table colgroup+thead tr:first-child th,.table thead:first-child tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child td{border-top:0}
 .table tbody+tbody{border-top:2px solid #d6b161}
 .table .table{background-color:#fff}
+.uploadhead{height:10%; text-align:left; max-height:20px; line-height:18px;  margin-bottom: 5px;}
+.uploadfoot{height:5%; text-align:center;}
+.uploadhead .fftext{font-weight: bold;}
+.uploadhead .select2-container .select2-choice .select2-arrow b{background-position:0 -3px}
+.uploadhead .extension{width:100px;min-width:100px;font-size:11px}
+.uploadhead .select2-container .select2-choice{max-height:20px;line-height:18px;text-align:center; font-weight: normal;}
 .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px}
 .table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161}
 .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px}
@@ -1370,7 +1376,7 @@ label{font-weight:normal}
 .upload-icon{font-size:1.2em;width:1.2em}
 .upload-icon-button{font-size:1.2em;width:1.2em;cursor:pointer}
 .upload-info{font-weight:normal;text-align:center}
-.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%}
+.upload-box{width:100%;height:85%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%}
 .upload-box .table th{text-align:center;white-space:nowrap}
 .upload-box .table td{margin:0px}
 .upload-box .upload-item .select2-arrow b{background-position:0 -3px}