Add an annotation or notes to this step; annotations are available when a workflow is viewed.
"),b&&"tool"==b.type){pjastr="
Edit Step Actions
"+display_pja_list()+" "+display_file_list(b)+"
Create
",pjastr+="
Add actions to this step; actions are applied when this workflow step completes.
",$("#right-content").find(".toolForm").after(pjastr);for(var c in b.post_job_actions)"undefined"!=c&&display_pja(b.post_job_actions[c],b);$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){workflow.active_form_has_changes=!1,b.update_field_data(a),show_workflow_parameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:b.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find("select[refresh_on_change='true']").change(function(){$(a).submit()}),$(this).find("input[refresh_on_change='true']").change(function(){$(a).submit()}),$(this).find(".popupmenu").each(function(){var b=$(this).parents("div.form-row").attr("id"),c=$('▼'),d={};$(this).find("button").each(function(){var b=$(this).attr("name"),c=$(this).attr("value");d[$(this).text()]=function(){$(a).append("").submit()}}),c.insertAfter(this),$(this).remove(),make_popupmenu(c,d)}),$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=!0})})})}$(function(){function a(){workflow.layout(),workflow.fit_canvas_to_nodes(),scroll_to_nodes(),canvas_manager.draw_overview()}function b(){workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function c(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}if(window.lt_ie_7)return void show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)reset_tool_search(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show();var b=galaxy_config.root+"api/tools";this.timer=setTimeout(function(){$.get(b,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview")),reset(),$.ajax({url:get_datatypes_url,dataType:"json",cache:!1,success:function(a){populate_datatype_info(a),$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:!1,success:function(a){reset(),workflow.from_simple(a),workflow.has_changes=!1,workflow.fit_canvas_to_nodes(),scroll_to_nodes(),canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="
"}),upgrade_message?show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.
"+upgrade_message+"
",{Continue:hide_modal}):hide_modal(),show_workflow_parameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}})}}),$(document).ajaxStart(function(){active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":b,"Auto Re-layout":a,Close:close_editor}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?d():c(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?d():c()}),window.onbeforeunload=function(){return workflow&&workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("");var e=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(e&&e.slideUp("fast"),e=a,a.slideDown("fast")):(a.slideUp("fast"),e=null)})}),async_save_text("workflow-name","workflow-name",rename_async_url,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,!0,4)});var close_editor=function(){workflow.check_changes_in_active_form(),workflow&&workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=workflow_index_url},show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})):window.document.location=workflow_index_url},save_current_workflow=function(a,b){if(show_message("Saving workflow","progress"),workflow.check_changes_in_active_form(),!workflow.has_changes)return hide_modal(),void(b&&b());workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("
Add an annotation or notes to this step; annotations are available when a workflow is viewed.
"),b&&"tool"==b.type){pjastr="
Edit Step Actions
"+display_pja_list()+" "+display_file_list(b)+"
Create
",pjastr+="
Add actions to this step; actions are applied when this workflow step completes.
",$("#right-content").find(".toolForm").after(pjastr);for(var c in b.post_job_actions)"undefined"!=c&&display_pja(b.post_job_actions[c],b);$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){workflow.active_form_has_changes=!1,b.update_field_data(a),show_workflow_parameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:b.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find("select[refresh_on_change='true']").change(function(){$(a).submit()}),$(this).find("input[refresh_on_change='true']").change(function(){$(a).submit()}),$(this).find(".popupmenu").each(function(){var b=$(this).parents("div.form-row").attr("id"),c=$('▼'),d={};$(this).find("button").each(function(){var b=$(this).attr("name"),c=$(this).attr("value");d[$(this).text()]=function(){$(a).append("").submit()}}),c.insertAfter(this),$(this).remove(),make_popupmenu(c,d)}),$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=!0})})})}$(function(){function a(){workflow.layout(),workflow.fit_canvas_to_nodes(),scroll_to_nodes(),canvas_manager.draw_overview()}function b(){workflow.clear_active_node(function(){$(".right-content").hide(),$("#edit-attributes").show()})}function c(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}if(window.lt_ie_7)return void show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)reset_tool_search(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show();var b=galaxy_config.root+"api/tools";this.timer=setTimeout(function(){$.get(b,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview")),reset(),datatypes=JSON.parse($.ajax({type:"GET",url:galaxy_config.root+"api/datatypes",async:!1}).responseText),$.ajax({url:get_datatypes_url,dataType:"json",cache:!1,success:function(a){populate_datatype_info(a),$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:!1,success:function(a){reset(),workflow.from_simple(a),workflow.has_changes=!1,workflow.fit_canvas_to_nodes(),scroll_to_nodes(),canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="
"}),upgrade_message?show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.
"+upgrade_message+"
",{Continue:hide_modal}):hide_modal(),show_workflow_parameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}})}}),$(document).ajaxStart(function(){active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":b,"Auto Re-layout":a,Close:close_editor}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?d():c(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?d():c()}),window.onbeforeunload=function(){return workflow&&workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("");var e=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(e&&e.slideUp("fast"),e=a,a.slideDown("fast")):(a.slideUp("fast"),e=null)})}),async_save_text("workflow-name","workflow-name",rename_async_url,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,!0,4)});var close_editor=function(){workflow.check_changes_in_active_form(),workflow&&workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=workflow_index_url},show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})):window.document.location=workflow_index_url},save_current_workflow=function(a,b){if(show_message("Saving workflow","progress"),workflow.check_changes_in_active_form(),!workflow.has_changes)return hide_modal(),void(b&&b());workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("
");$.each(b.errors,function(a,b){$("").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");workflow.name=b.name,workflow.has_changes=!1,workflow.stored=!0,show_workflow_parameters(),b.errors?show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),active_ajax_call=!1}):c(b)};
//# sourceMappingURL=../maps/galaxy.workflows.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js
index 4e9536f837d..ca2b7fc7b9d 100644
--- a/static/scripts/mvc/tools/tools-form-base.js
+++ b/static/scripts/mvc/tools/tools-form-base.js
@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement(""),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$(""),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement(""),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$(""),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/tools/tools-form-workflow.js b/static/scripts/mvc/tools/tools-form-workflow.js
index 9d8dd1070f0..3d0a6f95820 100644
--- a/static/scripts/mvc/tools/tools-form-workflow.js
+++ b/static/scripts/mvc/tools/tools-form-workflow.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=workflow.active_node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var g=b.inputs[e];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=f.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&c(g,d.slice(0))}}var d=[];for(key in b)d.push({0:b[key],1:b[key]});d.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},f=this;return c(e),e}});return{View:c}});
//# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map
\ No newline at end of file
diff --git a/static/scripts/utils/utils.js b/static/scripts/utils/utils.js
index e1c565c4f15..a43ae070835 100644
--- a/static/scripts/utils/utils.js
+++ b/static/scripts/utils/utils.js
@@ -1,2 +1,2 @@
-define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return $("").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('').appendTo("head")}function j(b,c){return b?a.defaults(b,c):c}function k(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"-";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:""+d+" "+c}function l(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function m(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:k,uid:l,time:m,request:g,sanitize:c,textify:e,validate:d,deepeach:b}});
+define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function d(a){return $("").text(a).html()}function e(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function f(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function g(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):h({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function h(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function i(a,b){var c=$('');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function j(a){$('link[href^="'+a+'"]').length||$('').appendTo("head")}function k(b,c){return b?a.defaults(b,c):c}function l(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"-";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:""+d+" "+c}function m(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function n(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:j,cssGetAttribute:i,get:g,merge:k,bytesToString:l,uid:m,time:n,request:h,sanitize:d,textify:f,validate:e,deepeach:b,isJSON:c}});
//# sourceMappingURL=../../maps/utils/utils.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index d272fc2c085..ee64bd443b5 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -22,6 +22,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
require(['mvc/tools/tools-form'], function(ToolsForm){
$(function(){
var form = new ToolsForm.View(${ h.dumps(self.form_config) });
+ $('body').append(form.$el);
});
});
diff --git a/templates/webapps/galaxy/workflow/editor.mako b/templates/webapps/galaxy/workflow/editor.mako
index 9575c99b74f..46aee1150ef 100644
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -14,16 +14,17 @@
-
${h.js( "libs/jquery/jquery.event.drag",
"libs/jquery/jquery.event.drop",
"libs/jquery/jquery.event.hover",
"libs/jquery/jquery.form",
"libs/jquery/jstorage",
+ "libs/jquery/jquery-ui",
"galaxy.workflow_editor.canvas",
"libs/jquery/jquery.autocomplete",
"galaxy.autocom_tagging",
- "galaxy.workflows" )}
+ "galaxy.workflows",
+ "libs/bibtex" )}
![]("+galaxy_config.root+"static/images/loading_small_white_bg.gif){kind=small}
loading tool info...