Merge branch 'wiki-to-hub' into dev

Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map

CITATION

@@ -16,7 +16,7 @@ following publications:
   a platform for interactive large-scale genome analysis." 
   Genome Research. 2005 Oct; 15(10):1451-5.
 
-See also: http://wiki.galaxyproject.org/CitingGalaxy
+See also: https://galaxyproject.org/citing-galaxy
 
 
 

client/galaxy/scripts/mvc/citation/citation-view.js

@@ -151,7 +151,7 @@ var CitationListView = Backbone.View.extend({
                 ' citations explicitly at this time. When writing up your analysis, please manually',
                 ' review your histories and find all references',
                 ' that should be cited in order to completely describe your work. Also, please remember to',
-                ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',
+                ' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',
                 '</div>',
             ].join('');
         } else {

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({
       '</table>',
       '<div class="empty-folder-message" style="display:none;">',
           'This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up',
-          ' please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
+          ' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
           ' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
       '</div>'
       ].join(''));

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -1151,7 +1151,7 @@ var FolderToolbarView = Backbone.View.extend({
               ' Details',
             '</button>',
             '<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
-              '<a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank">',
+              '<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">',
                 '<button class="primary-button" type="button">',
                   '<span class="fa fa-question-circle"></span>',
                   '&nbsp;Help',

client/galaxy/scripts/mvc/library/library-librarylist-view.js

@@ -232,7 +232,7 @@ var LibraryListView = Backbone.View.extend({
           '<% } else{ %>',
             '<div>',
               'There are no libraries visible to you here. If you expected some to show up please consult the',
-              ' <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
+              ' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
               ' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
             '</div>',
           '<% }%>',

client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js

@@ -192,7 +192,7 @@ var LibraryToolbarView = Backbone.View.extend({
                 '</span>',
               '<% } %>',
               '<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
-                '<a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank">',
+                '<a href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">',
                   '<button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button>',
                 '</a>',
               '</span>',

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -279,7 +279,7 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
                 _.each( options.requirements, function( req, i ) {
                     requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) );
                 });
-                var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://wiki.galaxyproject.org/Tools/Requirements' ).text( 'here' );
+                var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' );
                 return $( '<span/>' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' );
             }
             return 'No requirements found.';

client/galaxy/scripts/mvc/user/user-preferences.js

@@ -153,7 +153,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
             return  '<p class="ui-panel-footer">' +
                         'You are using <strong>' + options.nice_total_disk_usage + '</strong> of disk space in this Galaxy instance. ' +
                         ( Galaxy.config.enable_quotas ? 'Your disk quota is: <strong>' + options.quota + '</strong>. ' : '' ) +
-                        'Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
+                        'Is your usage more than expected? See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
                     '</p>';
         }
     });

client/galaxy/scripts/mvc/workflow/workflow-forms.js

@@ -151,7 +151,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
                     type        : 'text',
                     value       : '',
                     ignore      : '',
-                    help        : 'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
+                    help        : 'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
                 },{
                     action      : 'ChangeDatatypeAction',
                     pja_arg     : 'newtype',

client/galaxy/scripts/viz/phyloviz.js

@@ -741,7 +741,7 @@ var HeaderButtons = Backbone.View.extend({
                 $("#nodeSelectionView").show();
             } },
             { icon_class: 'information', title: 'Phyloviz Help', on_click: function() {
-                window.open('https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree');
+                window.open('https://galaxyproject.org/learn/visualization/phylogenetic-tree/');
                 // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit
             } }
         ],

config/galaxy.ini.sample

@@ -11,9 +11,10 @@
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
 #
-# Examples of many of these options are explained in more detail in the wiki:
+# Examples of many of these options are explained in more detail in the Galaxy
+# Community Hub.
 #
-#   https://wiki.galaxyproject.org/Admin/Config
+#   https://galaxyproject.org/admin/config
 #
 # Config hackers are encouraged to check there before asking for help.
 
@@ -179,7 +180,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Path to the directory in which tool dependencies are placed.  This is used by
 # the Tool Shed to install dependencies and can also be used by administrators
 # to manually install or link to dependencies.  For details, see:
-#   https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
+#   https://galaxyproject.org/admin/config/tool-dependencies
 # Set the string to None to explicitly disable tool dependency handling.
 # If this option is set to none or an invalid path, installing tools with dependencies
 # from the Tool Shed will fail.
@@ -305,9 +306,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # applied to the ToolDataTableManager at server start up.
 #shed_tool_data_table_config = config/shed_tool_data_table_conf.xml
 
-# Directory where data used by tools is located, see the samples in that
-# directory and the wiki for help:
-#   https://wiki.galaxyproject.org/Admin/DataIntegration
+# Directory where data used by tools is located.  See the samples in that
+# directory and the Galaxy Community Hub for help:
+# https://galaxyproject.org/admin/data-integration
 #tool_data_path = tool-data
 
 # Directory where Tool Data Table related files will be placed
@@ -483,7 +484,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 
 # URL of the support resource for the galaxy instance.  Used in activation
 # emails.
-#instance_resource_url = https://wiki.galaxyproject.org/
+#instance_resource_url = https://galaxyproject.org/
 
 # E-mail domains blacklist is used for filtering out users that are using
 # disposable email address during the registration.  If their address domain
@@ -544,7 +545,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # bypass security to display datasets.  Please be aware that there are security
 # implications if this is allowed.  More details (including required changes to
 # the proxy server config) are available in the Apache proxy documentation on
-# the wiki.
+# the Galaxy Community Hub.
 #
 # The list of servers in this sample config are for the UCSC Main, Test and
 # Archaea browsers, but the default if left commented is to not allow any
@@ -615,19 +616,19 @@ nglims_config_file = tool-data/nglims.yaml
 #logo_url = /
 
 # The URL linked by the "Wiki" link in the "Help" menu.
-#wiki_url = https://wiki.galaxyproject.org/
+#wiki_url = https://galaxyproject.org/
 
 # The URL linked by the "Support" link in the "Help" menu.
-#support_url = https://wiki.galaxyproject.org/Support
+#support_url = https://galaxyproject.org/support
 
 # The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
-#citation_url = https://wiki.galaxyproject.org/CitingGalaxy
+#citation_url = https://galaxyproject.org/citing-galaxy
 
 # The URL linked by the "Search" link in the "Help" menu.
-#search_url = http://galaxyproject.org/search/usegalaxy/
+#search_url = https://galaxyproject.org/search/
 
 # The URL linked by the "Mailing Lists" link in the "Help" menu.
-#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists
+#mailing_lists_url = https://galaxyproject.org/mailing-lists
 
 # The URL linked by the "Videos" link in the "Help" menu.
 #screencasts_url = https://vimeo.com/galaxyproject
@@ -892,8 +893,9 @@ use_interactive = True
 
 # -- Data Libraries
 
-# These library upload options are described in much more detail in the wiki:
-#   https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
+# These library upload options are described in much more detail in the Galaxy
+# Community Hub:
+# https://galaxyproject.org/data-libraries/
 
 # Add an option to the library upload form which allows administrators to
 # upload a directory of files.
@@ -979,7 +981,7 @@ use_interactive = True
 # User authentication can be delegated to an upstream proxy server (usually
 # Apache).  The upstream proxy should set a REMOTE_USER header in the request.
 # Enabling remote user disables regular logins.  For more information, see:
-#   https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
+#   https://galaxyproject.org/admin/config/apache-proxy
 #use_remote_user = False
 
 # If use_remote_user is enabled and your external authentication
@@ -1022,7 +1024,7 @@ use_interactive = True
 # users (email addresses).  These users will have access to the Admin section
 # of the server, and will have access to create users, groups, roles,
 # libraries, and more.  For more information, see:
-#   https://wiki.galaxyproject.org/Admin/Interface
+#   https://galaxyproject.org/admin/
 #admin_users = None
 
 # Force everyone to log in (disable anonymous access).
@@ -1213,7 +1215,7 @@ use_interactive = True
 # separate Galaxy into multiple processes.  There are more than one way to do
 # this, and they are explained in detail in the documentation:
 #
-#   https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
+#   https://galaxyproject.org/admin/config/performance/scaling
 
 # By default, Galaxy manages and executes jobs from within a single process and
 # notifies itself of new jobs via in-memory queues.  Jobs are run locally on
@@ -1302,7 +1304,7 @@ use_interactive = True
 # actual user instead of as the user running the Galaxy server process.  For
 # details on these options, see the documentation at:
 #
-# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
+# https://galaxyproject.org/admin/config/performance/cluster
 #
 #drmaa_external_runjob_script = scripts/drmaa_external_runner.py
 #drmaa_external_killjob_script = scripts/drmaa_external_killer.py

lib/galaxy/config.py

@@ -369,8 +369,9 @@ class Configuration( object ):
         self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
         self.message_box_content = kwargs.get( 'message_box_content', None )
         self.message_box_class = kwargs.get( 'message_box_class', 'info' )
-        self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
-        self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
+        self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' )
+        self.citation_url = kwargs.get( 'citation_url', 'https://galaxyproject.org/citing-galaxy' )
+        self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
         self.blog_url = kwargs.get( 'blog_url', None )
         self.screencasts_url = kwargs.get( 'screencasts_url', None )
         self.library_import_dir = kwargs.get( 'library_import_dir', None )

lib/galaxy/managers/configuration.py

@@ -41,13 +41,12 @@ class ConfigSerializer( base.ModelSerializer ):
             'logo_src'                          : lambda i, k, **c: self.url_for( '/static/images/galaxyIcon_noText.png' ),
             'terms_url'                         : _defaults_to( '' ),
 
-            # TODO: don't hardcode here - hardcode defaults once in config.py
-            'wiki_url'                          : _defaults_to( "http://galaxyproject.org/" ),
-            'search_url'                        : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
-            'mailing_lists'                     : _defaults_to( "https://wiki.galaxyproject.org/MailingLists" ),
+            'wiki_url'                          : _defaults_to( self.app.config.wiki_url ),
+            'search_url'                        : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/search/" ),
+            'mailing_lists'                     : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/mailing-lists/"),
             'screencasts_url'                   : _defaults_to( "https://vimeo.com/galaxyproject" ),
-            'citation_url'                      : _defaults_to( "https://wiki.galaxyproject.org/CitingGalaxy" ),
-            'support_url'                       : _defaults_to( "https://wiki.galaxyproject.org/Support" ),
+            'citation_url'                      : _defaults_to( self.app.config.citation_url ),
+            'support_url'                       : _defaults_to( self.app.config.support_url ),
             'lims_doc_url'                      : _defaults_to( "https://usegalaxy.org/u/rkchak/p/sts" ),
             'biostar_url'                       : _defaults_to( '' ),
             'biostar_url_redirect'              : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect', qualified=True ),

lib/galaxy/web/base/controllers/admin.py

@@ -1041,7 +1041,7 @@ class Admin( object ):
                 stop_msg += '.'
             for job_id in job_ids:
                 error_msg = "This job was stopped by an administrator: %s  <a href='%s' target='_blank'>Contact support</a> for additional help." \
-                    % ( stop_msg, self.app.config.get("support_url", "https://wiki.galaxyproject.org/Support" ) )
+                    % ( stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/" ) )
                 if trans.app.config.track_jobs_in_database:
                     job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
                     job.stderr = error_msg

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -33,8 +33,7 @@ def get_message_for_no_shed_tool_config():
     message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
     message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
     message += '<toolbox tool_path="../shed_tools">).  For details, see the "Installation of Galaxy tool shed repository tools into a local '
-    message += 'Galaxy instance" section of the Galaxy tool shed wiki at http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#'
-    message += 'Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance.'
+    message += 'Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
     return message
 
 

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -961,7 +961,7 @@ class AdminToolshed( AdminGalaxy ):
             message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
             message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
             message += 'whose <b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
-            message += '<a href="https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy" target="_blank">Installation '
+            message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
             message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
             message += 'Shed wiki for all of the details.'
             return trans.show_error_message( message )

lib/galaxy/webapps/reports/config.py

@@ -45,7 +45,7 @@ class Configuration( object ):
         self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
         self.message_box_content = kwargs.get( 'message_box_content', None )
         self.message_box_class = kwargs.get( 'message_box_class', 'info' )
-        self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
+        self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
         self.blog_url = kwargs.get( 'blog_url', None )
         self.screencasts_url = kwargs.get( 'screencasts_url', None )
         self.log_events = False

lib/galaxy/webapps/tool_shed/config.py

@@ -113,8 +113,8 @@ class Configuration( object ):
         self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
         self.message_box_content = kwargs.get( 'message_box_content', None )
         self.message_box_class = kwargs.get( 'message_box_class', 'info' )
-        self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
-        self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
+        self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' )
+        self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
         self.blog_url = kwargs.get( 'blog_url', None )
         self.biostar_url = kwargs.get( 'biostar_url', None )
         self.screencasts_url = kwargs.get( 'screencasts_url', None )

static/maps/mvc/citation/citation-view.js.map

@@ -1 +1 @@
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@@ -1,2 +1,2 @@
-define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,b,c){var d=Backbone.View.extend({tagName:"div",className:"citations",render:function(){return this.$el.append("<p>"+this.formattedReference()+"</p>"),this},formattedReference:function(){var a=this.model,b=a.entryType(),c=a.fields(),d="",e=this._asSentence((c.author?c.author:"")+(c.year?" ("+c.year+")":""))+" ",f=c.title||"",g=c.pages?"pp. "+c.pages:"",h=c.address;if("article"==b){var i=(c.volume?c.volume:"")+(c.number?" ("+c.number+")":"")+(g?", "+g:"");d=e+this._asSentence(f)+(c.journal?"In <em>"+c.journal+", ":"")+this._asSentence(i)+this._asSentence(c.address)+"</em>"}else d="inproceedings"==b||"proceedings"==b?e+this._asSentence(f)+(c.booktitle?"In <em>"+c.booktitle+", ":"")+(g?g:"")+(h?", "+h:"")+".</em>":"mastersthesis"==b||"phdthesis"==b?e+this._asSentence(f)+(c.howpublished?c.howpublished+". ":"")+(c.note?c.note+".":""):"techreport"==b?e+this._asSentence(f)+this._asSentence(c.institution)+this._asSentence(c.number)+this._asSentence(c.type):"book"==b||"inbook"==b||"incollection"==b?e+" "+this._formatBookInfo(c):e+" "+this._asSentence(f)+this._asSentence(c.howpublished)+this._asSentence(c.note);var j="";c.doi&&(j="http://dx.doi.org/"+c.doi,d+='[<a href="'+j+'" target="_blank">doi:'+c.doi+"</a>]");var k=c.url||j;return k&&(d+='[<a href="'+k+'" target="_blank">Link</a>]'),d},_formatBookInfo:function(a){var b="";return a.chapter&&(b+=a.chapter+" in "),a.title&&(b+="<em>"+a.title+"</em>"),a.editor&&(b+=", Edited by "+a.editor+", "),a.publisher&&(b+=", "+a.publisher),a.pages&&(b+=", pp. "+a.pages),a.series&&(b+=", <em>"+a.series+"</em>"),a.volume&&(b+=", Vol."+a.volume),a.issn&&(b+=", ISBN: "+a.issn),b+"."},_asSentence:function(a){return a&&a.trim()?a+". ":""}}),e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(a){var b=new d({model:a});this.$(".citations-formatted").append(b.render().el);var c=this.$(".citations-bibtex-text");c.val(c.val()+"\n\r"+a.attributes.content)},render:function(){this.$el.html(this.citationsElement()),this.collection.each(function(a){this.renderCitation(a)},this),this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show(),this.$(".citations-to-bibtex").hide(),this.$(".citations-bibtex").show(),this.$(".citations-formatted").hide(),this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide(),this.$(".citations-to-bibtex").show(),this.$(".citations-bibtex").hide(),this.$(".citations-formatted").show()},partialWarningElement:function(){return this.collection.partial?['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>"].join(""):""},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <button type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format."><i class="fa fa-pencil-square-o"></i> Show BibTeX</button>',' <button type="button" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list."><i class="fa fa-times"></i> Hide BibTeX</button>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted" style="word-wrap: break-word;"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:d,CitationListView:e}});
+define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,b,c){var d=Backbone.View.extend({tagName:"div",className:"citations",render:function(){return this.$el.append("<p>"+this.formattedReference()+"</p>"),this},formattedReference:function(){var a=this.model,b=a.entryType(),c=a.fields(),d="",e=this._asSentence((c.author?c.author:"")+(c.year?" ("+c.year+")":""))+" ",f=c.title||"",g=c.pages?"pp. "+c.pages:"",h=c.address;if("article"==b){var i=(c.volume?c.volume:"")+(c.number?" ("+c.number+")":"")+(g?", "+g:"");d=e+this._asSentence(f)+(c.journal?"In <em>"+c.journal+", ":"")+this._asSentence(i)+this._asSentence(c.address)+"</em>"}else d="inproceedings"==b||"proceedings"==b?e+this._asSentence(f)+(c.booktitle?"In <em>"+c.booktitle+", ":"")+(g?g:"")+(h?", "+h:"")+".</em>":"mastersthesis"==b||"phdthesis"==b?e+this._asSentence(f)+(c.howpublished?c.howpublished+". ":"")+(c.note?c.note+".":""):"techreport"==b?e+this._asSentence(f)+this._asSentence(c.institution)+this._asSentence(c.number)+this._asSentence(c.type):"book"==b||"inbook"==b||"incollection"==b?e+" "+this._formatBookInfo(c):e+" "+this._asSentence(f)+this._asSentence(c.howpublished)+this._asSentence(c.note);var j="";c.doi&&(j="http://dx.doi.org/"+c.doi,d+='[<a href="'+j+'" target="_blank">doi:'+c.doi+"</a>]");var k=c.url||j;return k&&(d+='[<a href="'+k+'" target="_blank">Link</a>]'),d},_formatBookInfo:function(a){var b="";return a.chapter&&(b+=a.chapter+" in "),a.title&&(b+="<em>"+a.title+"</em>"),a.editor&&(b+=", Edited by "+a.editor+", "),a.publisher&&(b+=", "+a.publisher),a.pages&&(b+=", pp. "+a.pages),a.series&&(b+=", <em>"+a.series+"</em>"),a.volume&&(b+=", Vol."+a.volume),a.issn&&(b+=", ISBN: "+a.issn),b+"."},_asSentence:function(a){return a&&a.trim()?a+". ":""}}),e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(a){var b=new d({model:a});this.$(".citations-formatted").append(b.render().el);var c=this.$(".citations-bibtex-text");c.val(c.val()+"\n\r"+a.attributes.content)},render:function(){this.$el.html(this.citationsElement()),this.collection.each(function(a){this.renderCitation(a)},this),this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show(),this.$(".citations-to-bibtex").hide(),this.$(".citations-bibtex").show(),this.$(".citations-formatted").hide(),this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide(),this.$(".citations-to-bibtex").show(),this.$(".citations-bibtex").hide(),this.$(".citations-formatted").show()},partialWarningElement:function(){return this.collection.partial?['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',"</div>"].join(""):""},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <button type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format."><i class="fa fa-pencil-square-o"></i> Show BibTeX</button>',' <button type="button" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list."><i class="fa fa-times"></i> Hide BibTeX</button>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted" style="word-wrap: break-word;"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:d,CitationListView:e}});
 //# sourceMappingURL=../../../maps/mvc/citation/citation-view.js.map

static/scripts/mvc/library/library-librarylist-view.js

@@ -1,2 +1,2 @@
-define(["layout/masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view","libs/underscore"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(a){this.options=g.defaults(this.options||{},a,this.defaults);var b=this;this.modal=null,this.collection=new e.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){b.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},render:function(a){this.options=g.extend(this.options,a),this.setElement("#libraries_element");var b=this.templateLibraryList(),c=null,d=null;if($(".tooltip").hide(),"undefined"!=typeof a&&(d="undefined"!=typeof a.models?a.models:null),null!==this.collection&&null===d)this.sortLibraries(),c=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1});else if(null!==d)if(Galaxy.libraries.preferences.get("with_deleted"))c=d;else{var e=function(a){return a.get("deleted")===!1};c=g.filter(d,e)}else c=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=c.length;var f=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&f<this.options.total_libraries_count?(c=c.slice(f,f+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=c.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(c=[]),this.$el.html(b({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(c)):(this.$el.html(b({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var a=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){a.options.all_fetched=!0,a.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({library:c})}},renderOne:function(a){var b=a.library,c=new f.LibraryRowView(b);this.$el.find("#library_list_body").append(c.el)},sort_clicked:function(){Galaxy.libraries.preferences.set("asc"===Galaxy.libraries.preferences.get("sort_order")?{sort_order:"desc"}:{sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortByNameAsc():"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortByNameDesc())},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},searchLibraries:function(a){var b=$.trim(a);if(""!==b){var c=null;c=this.collection.search(a),this.options.searching=!0,this.render({models:c})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return g.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});return{LibraryListView:h}});
+define(["layout/masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view","libs/underscore"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(a){this.options=g.defaults(this.options||{},a,this.defaults);var b=this;this.modal=null,this.collection=new e.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){b.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},render:function(a){this.options=g.extend(this.options,a),this.setElement("#libraries_element");var b=this.templateLibraryList(),c=null,d=null;if($(".tooltip").hide(),"undefined"!=typeof a&&(d="undefined"!=typeof a.models?a.models:null),null!==this.collection&&null===d)this.sortLibraries(),c=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1});else if(null!==d)if(Galaxy.libraries.preferences.get("with_deleted"))c=d;else{var e=function(a){return a.get("deleted")===!1};c=g.filter(d,e)}else c=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=c.length;var f=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&f<this.options.total_libraries_count?(c=c.slice(f,f+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=c.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(c=[]),this.$el.html(b({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(c)):(this.$el.html(b({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var a=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){a.options.all_fetched=!0,a.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({library:c})}},renderOne:function(a){var b=a.library,c=new f.LibraryRowView(b);this.$el.find("#library_list_body").append(c.el)},sort_clicked:function(){Galaxy.libraries.preferences.set("asc"===Galaxy.libraries.preferences.get("sort_order")?{sort_order:"desc"}:{sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortByNameAsc():"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortByNameDesc())},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},searchLibraries:function(a){var b=$.trim(a);if(""!==b){var c=null;c=this.collection.search(a),this.options.searching=!0,this.render({models:c})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return g.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});return{LibraryListView:h}});
 //# sourceMappingURL=../../../maps/mvc/library/library-librarylist-view.js.map

static/scripts/mvc/workflow/workflow-forms.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){this.form=new b(a)}}),e=Backbone.View.extend({initialize:function(b){var d=this;this.workflow=b.workflow,this.node=b.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},a.deepeach(b.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions)+")",b.value={__class__:"RuntimeValue"}):b.fixed||(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(b.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(b),this.form=new c(a.merge(b,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",postchange:function(b,c){var e=c.model.attributes,f={tool_id:e.id,tool_version:e.version,type:"tool",inputs:$.extend(!0,{},c.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",f),a.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:f,success:function(a){c.update(a.config_form),c.errors(a.config_form),d.node.update_field_data(a),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",a),b.reject()}})}}))):Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(a){var b=a.inputs,c=a.datatypes,d=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(d){b.push({name:"pja__"+d+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+d])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),b.push({name:"pja__"+d+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+d])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var e in this.node.output_terminals)b.push(this._makeSection(e,c))}},_makeSection:function(a,b){function c(b,e){e=e||[],e.push(b);for(var f in b.inputs){var g=b.inputs[f],h=g.action;if(h){if(g.name="pja__"+a+"__"+g.action,g.pja_arg&&(g.name+="__"+g.pja_arg),g.payload)for(var i in g.payload){var j=g.payload[i];g.payload[g.name+"__"+i]=j,delete j}var k=d.post_job_actions[g.action+a];if(k){for(var l in e)e[l].expanded=!0;g.value=g.pja_arg?k.action_arguments&&k.action_arguments[g.pja_arg]||g.value:"true"}}g.inputs&&c(g,e.slice(0))}}var d=this,e=[],f=[];for(key in b)e.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)f.push(this.node.input_terminals[key].name);e.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),e.unshift({0:"Sequences",1:"Sequences"}),e.unshift({0:"Roadmaps",1:"Roadmaps"}),e.unshift({0:"Leave unchanged",1:"__empty__"});var g={title:"Configure Output: '"+a+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(output=this.node.getWorkflowOutput(a))&&output.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(b){d.workflow.attemptUpdateOutputLabel(d.node,a,b)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+f.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:e,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"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",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return c(g),g}});return{Default:d,Tool:e}});
+define(["utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){this.form=new b(a)}}),e=Backbone.View.extend({initialize:function(b){var d=this;this.workflow=b.workflow,this.node=b.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},a.deepeach(b.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions)+")",b.value={__class__:"RuntimeValue"}):b.fixed||(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(b.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(b),this.form=new c(a.merge(b,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",postchange:function(b,c){var e=c.model.attributes,f={tool_id:e.id,tool_version:e.version,type:"tool",inputs:$.extend(!0,{},c.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",f),a.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:f,success:function(a){c.update(a.config_form),c.errors(a.config_form),d.node.update_field_data(a),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",a),b.reject()}})}}))):Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(a){var b=a.inputs,c=a.datatypes,d=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(d){b.push({name:"pja__"+d+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+d])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),b.push({name:"pja__"+d+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+d])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var e in this.node.output_terminals)b.push(this._makeSection(e,c))}},_makeSection:function(a,b){function c(b,e){e=e||[],e.push(b);for(var f in b.inputs){var g=b.inputs[f],h=g.action;if(h){if(g.name="pja__"+a+"__"+g.action,g.pja_arg&&(g.name+="__"+g.pja_arg),g.payload)for(var i in g.payload){var j=g.payload[i];g.payload[g.name+"__"+i]=j,delete j}var k=d.post_job_actions[g.action+a];if(k){for(var l in e)e[l].expanded=!0;g.value=g.pja_arg?k.action_arguments&&k.action_arguments[g.pja_arg]||g.value:"true"}}g.inputs&&c(g,e.slice(0))}}var d=this,e=[],f=[];for(key in b)e.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)f.push(this.node.input_terminals[key].name);e.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),e.unshift({0:"Sequences",1:"Sequences"}),e.unshift({0:"Roadmaps",1:"Roadmaps"}),e.unshift({0:"Leave unchanged",1:"__empty__"});var g={title:"Configure Output: '"+a+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(output=this.node.getWorkflowOutput(a))&&output.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(b){d.workflow.attemptUpdateOutputLabel(d.node,a,b)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>'+f.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:e,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"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",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return c(g),g}});return{Default:d,Tool:e}});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-forms.js.map

templates/admin/tool_shed_repository/select_tool_panel_section.mako

@@ -51,11 +51,11 @@
         repository tools may include code that produces malicious behavior, so be aware of what you are installing.
     </p>
     <p>
-        If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/Support" target="_blank">Galaxy support</a>,
+        If you discover a repository that causes problems after installation, contact <a href="https://galaxyproject.org/support" target="_blank">Galaxy support</a>,
         sending all necessary information, and appropriate action will be taken.
     </p>
     <p>
-        <a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repository_owner" target="_blank">Contact the repository owner</a> for
+        <a href="https://galaxyproject.org/toolshed/repository-features/#contact-repository-owner" target="_blank">Contact the repository owner</a> for
         general questions or concerns.
     </p>
 </div>

templates/user/index.mako

@@ -33,7 +33,7 @@
             %if trans.app.config.enable_quotas:
                 Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>.
             %endif
-            Is your usage more than expected?  See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.
+            Is your usage more than expected?  See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.
         </p>
     %endif
 %else:

templates/webapps/galaxy/admin/center.mako

@@ -4,7 +4,7 @@
 <%def name="title()">Galaxy Administration</%def>
 
 <h2>Administration</h2>
-Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the Galaxy administration hub</a> to learn how to keep your Galaxy in best shape.
+Please visit <a href="https://galaxyproject.org/admin" target="_blank">the Galaxy administration hub</a> to learn how to keep your Galaxy in best shape.
 %if message:
     ${render_msg( message, status )}
 %else:
@@ -28,7 +28,7 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
             <ul>
             %if trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds:
                 <li>
-                    <strong>Search Tool Shed</strong> - Search and install new tools and other Galaxy utilities from the Tool Shed. See <a href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial" target="_blank">the tutorial</a>.
+                    <strong>Search Tool Shed</strong> - Search and install new tools and other Galaxy utilities from the Tool Shed. See <a href="https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial" target="_blank">the tutorial</a>.
                 </li>
             %endif
             %if tool_shed_repository_ids:
@@ -84,14 +84,14 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
             <ul>
             %if trans.app.config.enable_quotas:
                 <li>
-                    <strong>Quotas</strong> - Manage user space quotas. See <a href="https://wiki.galaxyproject.org/Admin/DiskQuotas" target="_blank">wiki</a> for details.
+                    <strong>Quotas</strong> - Manage user space quotas. See <a href="https://galaxyproject.org/admin/disk-quotas" target="_blank">wiki</a> for details.
                 </li>
             %endif
                 <li>
-                    <strong>Data libraries</strong> - Data libraries enable authorized Galaxy users to share datasets with other groups or users. Only administrators can create data libraries. See <a href="https://wiki.galaxyproject.org/DataLibraries" target="_blank">wiki</a> for details and <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">this page</a> for security description.
+                    <strong>Data libraries</strong> - Data libraries enable authorized Galaxy users to share datasets with other groups or users. Only administrators can create data libraries. See <a href="https://galaxyproject.org/data-libraries" target="_blank">wiki</a> for details.
                 </li>
                 <li>
-                    <strong>Local data</strong> - Manage the reference (and other) data that is stored within Tool Data Tables. See <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki</a> for details.
+                    <strong>Local data</strong> - Manage the reference (and other) data that is stored within Tool Data Tables. See <a href="https://galaxyproject.org/admin/tools/data-managers" target="_blank">wiki</a> for details.
                 </li>
             </ul>
         <h4>Form definitions</h4>
@@ -104,7 +104,7 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
         <h4>Sample tracking</h4>
             <ul>
                 <li>
-                    Please see the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySampleTracking" target="_blank">sample tracking tutorial</a>.
+                    Please see the <a href="https://galaxyproject.org/archive/library-sample-tracking" target="_blank">sample tracking tutorial</a>.
                 </li>
             </ul>
 %endif

templates/webapps/galaxy/data_manager/index.mako

@@ -67,4 +67,4 @@
     <br/>
 %endif
 
-${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki.</a>', "info" ) }
+${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://galaxyproject.org/admin/tools/data-managers/" target="_blank">wiki.</a>', "info" ) }

templates/webapps/galaxy/galaxy.masthead.mako

@@ -15,12 +15,12 @@
             'lims_doc_url'              : app.config.get("lims_doc_url", "https://usegalaxy.org/u/rkchak/p/sts"),
             'biostar_url'               : app.config.biostar_url,
             'biostar_url_redirect'      : h.url_for( controller='biostar', action='biostar_redirect', qualified=True ),
-            'support_url'               : app.config.get("support_url", "https://wiki.galaxyproject.org/Support"),
-            'search_url'                : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"),
-            'mailing_lists'             : app.config.get("mailing_lists", "https://wiki.galaxyproject.org/MailingLists"),
+            'support_url'               : app.config.get("support_url", "https://galaxyproject.org/support"),
+            'search_url'                : app.config.get("search_url", "http://galaxyproject.org/search/"),
+            'mailing_lists'             : app.config.get("mailing_lists", "https://galaxyproject.org/mailing-lists"),
             'screencasts_url'           : app.config.get("screencasts_url", "https://vimeo.com/galaxyproject"),
-            'wiki_url'                  : app.config.get("wiki_url", "https://wiki.galaxyproject.org/"),
-            'citation_url'              : app.config.get("citation_url", "https://wiki.galaxyproject.org/CitingGalaxy"),
+            'wiki_url'                  : app.config.get("wiki_url", "https://galaxyproject.org/"),
+            'citation_url'              : app.config.get("citation_url", "https://galaxyproject.org/citing-galaxy"),
             'terms_url'                 : app.config.get("terms_url", ""),
             'allow_user_creation'       : app.config.allow_user_creation,
             'logo_url'                  : h.url_for(app.config.get( 'logo_url', '/')),
@@ -78,4 +78,4 @@
             });
         });
     </script>
-</%def>
+</%def>

templates/webapps/tool_shed/base_panels.mako

@@ -115,13 +115,13 @@
                     if qa_url:
                         menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ]
                     menu_options.extend( [
-                        [_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ],
-                        [_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ],
-                        [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ],
-                        [_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://wiki.galaxyproject.org/MailingLists" ), "_blank" ],
+                        [_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://galaxyproject.org/toolshed" ), "_blank" ],
+                        [_('Support'), app.config.get( "support_url", "https://galaxyproject.org/support" ), "_blank" ],
+                        [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/" ), "_blank" ],
+                        [_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://galaxyproject.org/mailing-lists" ), "_blank" ],
                         [_('Videos'), app.config.get( "screencasts_url", "https://vimeo.com/galaxyproject" ), "_blank" ],
                         [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ],
-                        [_('How to Cite Galaxy'), app.config.get( "citation_url", "https://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ]
+                        [_('How to Cite Galaxy'), app.config.get( "citation_url", "https://galaxyproject.org/citing-galaxy" ), "_blank" ]
                     ] )
                     tab( "help", _("Help"), None, menu_options=menu_options )
                 %>

test/qunit/tests/form_tests.js

@@ -29,7 +29,7 @@ define([ 'test-app', 'mvc/form/form-input', 'mvc/ui/ui-misc', 'mvc/form/form-dat
         ok( dropdown.children().length == 2, 'Found two menu items' );
         dropdown.find( '.fa-info-circle' ).parent().click();
         this.clock.tick ( window.WAIT_FADE );
-        ok( form.$( '.ui-message' ).html() === '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.</span>', 'Check requirements message' );
+        ok( form.$( '.ui-message' ).html() === '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://galaxyproject.org/tools/requirements/">here</a> for more information.</span>', 'Check requirements message' );
         ok( form.$( '.form-repeat-delete' ).css( 'display' ) == 'none', 'Delete button disabled' );
         var $add = form.$( '.form-repeat-add' );
         ok( !$add.attr( 'disabled' ), 'Adding new repeat possible' );
@@ -101,4 +101,4 @@ define([ 'test-app', 'mvc/form/form-input', 'mvc/ui/ui-misc', 'mvc/form/form-dat
         input.model.set( 'help', '_help (_argument)' );
         ok( input.$info.html() == '_help (_argument)', 'Correct help text with argument from help' );
     } );
-});
+});