- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Allow GenomeSpace OpenID provider for log in.
by Bitbucket 13 Apr '12

13 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/52c03c6b8f29/ changeset: 52c03c6b8f29 user: dan date: 2012-04-13 21:07:07 summary: Allow GenomeSpace OpenID provider for log in. affected #: 1 file diff -r 6fb1b84b81c3bb146674a3387d1358aa753bad31 -r 52c03c6b8f29a919a7bb19d7c414e65f611b9907 openid/genomespace.xml --- a/openid/genomespace.xml +++ b/openid/genomespace.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<provider id="genomespace" name="GenomeSpace" never_associate_with_user="True"> +<provider id="genomespace" name="GenomeSpace"><op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url><sreg><field name="nickname" required="True"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Tweek for empty referer value causing OpenID verification failure.
by Bitbucket 13 Apr '12

13 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6fb1b84b81c3/ changeset: 6fb1b84b81c3 user: dan date: 2012-04-13 16:13:08 summary: Tweek for empty referer value causing OpenID verification failure. affected #: 1 file diff -r afd1b16d7ec5d86dbe4f4a8d8636ec1d82d49f98 -r 6fb1b84b81c3bb146674a3387d1358aa753bad31 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -56,7 +56,7 @@ openid_provider = kwd.get( 'openid_provider', '' ) if not openid_provider or openid_url: openid_provider = trans.app.openid_providers.NO_PROVIDER_ID #empty fields cause validation errors - redirect = kwd.get( 'redirect', '' ) + redirect = kwd.get( 'redirect', '' ).strip() auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) action = 'login' @@ -68,7 +68,9 @@ if not openid_url and openid_provider == trans.app.openid_providers.NO_PROVIDER_ID: message = 'An OpenID provider was not specified' elif openid_provider_obj: - process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', redirect=redirect, openid_provider=openid_provider, auto_associate=auto_associate ) + if not redirect: + redirect = ' ' + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', redirect=redirect, openid_provider=openid_provider, auto_associate=auto_associate ) #None of these values can be empty, or else a verification error will occur request = None try: request = consumer.begin( openid_provider_obj.op_endpoint_url ) @@ -111,7 +113,7 @@ consumer = trans.app.openid_manager.get_consumer( trans ) info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() - redirect = kwd.get( 'redirect', '' ) + redirect = kwd.get( 'redirect', '' ).strip() openid_provider = kwd.get( 'openid_provider', None ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) @@ -223,7 +225,7 @@ status = kwd.get( 'status', 'done' ) email = kwd.get( 'email', '' ) username = kwd.get( 'username', '' ) - redirect = kwd.get( 'redirect', '' ) + redirect = kwd.get( 'redirect', '' ).strip() params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() openids = trans.galaxy_session.openids @@ -408,13 +410,13 @@ use_panels=use_panels, id=kwd['id'] ) ) - kwd['redirect'] = kwd.get( 'redirect', url_for( controller='user', action='openid_manage', use_panels=True ) ) + kwd['redirect'] = kwd.get( 'redirect', url_for( controller='user', action='openid_manage', use_panels=True ) ).strip() kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): '''Handle Galaxy Log in''' - redirect = kwd.get( 'redirect', trans.request.referer ) + redirect = kwd.get( 'redirect', trans.request.referer ).strip() use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -462,7 +464,7 @@ status = kwd.get( 'status', 'done' ) email = kwd.get( 'email', '' ) password = kwd.get( 'password', '' ) - redirect = kwd.get( 'redirect', trans.request.referer ) + redirect = kwd.get( 'redirect', trans.request.referer ).strip() success = False user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() if not user: @@ -522,7 +524,7 @@ username = util.restore_text( params.get( 'username', '' ) ) subscribe = params.get( 'subscribe', '' ) subscribe_checked = CheckboxField.is_checked( subscribe ) - redirect = kwd.get( 'redirect', trans.request.referer ) + redirect = kwd.get( 'redirect', trans.request.referer ).strip() is_admin = cntrller == 'admin' and trans.user_is_admin if not trans.app.config.allow_user_creation and not trans.user_is_admin(): message = 'User registration is disabled. Please contact your Galaxy administrator for an account.' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 7 new changesets
by Bitbucket 13 Apr '12

13 Apr '12

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f11e8aa26fcc/ changeset: f11e8aa26fcc user: jgoecks date: 2012-04-12 20:14:00 summary: More client-side support for tools: (a) include different attributes in dict depending on params; (b) framework for dictifying inputs; (c) support for getting tool description by id via API. affected #: 2 files diff -r 84d49e39069d965a45097ade1b71a57cdc0a0386 -r f11e8aa26fcc88b9fa92e752000b092cfefce88c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -598,7 +598,7 @@ """ Return a dict that includes section's attributes. """ section_elts = [] for key, val in self.elems.items(): - section_elts.append( val.to_dict( trans ) ) + section_elts.append( val.to_dict( trans, for_link=True ) ) return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts } class ToolSectionLabel( object ): @@ -611,7 +611,7 @@ self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' - def to_dict( self, trans ): + def to_dict( self, trans, **kwargs ): """ Return a dict that includes label's attributes. """ return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version } @@ -691,6 +691,14 @@ def __iter__( self ): return iter( ( self.format, self.metadata_source, self.parent ) ) + + def to_dict( self ): + return { + 'name': self.name, + 'format': self.format, + 'label': self.label, + 'hidden': self.hidden + } class ToolRequirement( object ): """ @@ -2392,20 +2400,48 @@ return True return False - def to_dict( self, trans ): - """ Return dict of tool attributes. """ + def to_dict( self, trans, for_link=False, for_display=False ): + """ Returns dict of tool. """ - # Create tool link. - if not self.tool_type.startswith( 'data_source' ): - link = url_for( controller='tool_runner', tool_id=self.id ) - else: - link = url_for( self.action, **self.get_static_param_values( trans ) ) + # Basic information + tool_dict = { 'id': self.id, 'name': self.name, + 'version': self.version, 'description': self.description } + + if for_link: + # Create tool link. + if not self.tool_type.startswith( 'data_source' ): + link = url_for( controller='tool_runner', tool_id=self.id ) + else: + link = url_for( self.action, **self.get_static_param_values( trans ) ) - return { 'type': 'tool', 'id': self.id, 'name': self.name, 'link': link, - 'version': self.version, 'description': self.description, - 'min_width': self.uihints.get( 'minwidth', -1 ), - 'target': self.target, - 'hidden': self._is_hidden_for_user( trans.user ) } + # Basic information + tool_dict.update( { 'type': 'tool', 'link': link, + 'min_width': self.uihints.get( 'minwidth', -1 ), + 'target': self.target } ) + + if for_display: + # Dictify inputs. + inputs = [] + for name, input in self.inputs.items(): + param_dict = { 'name' : name, 'label' : input.label } + if isinstance( input, DataToolParameter ): + param_dict.update( { 'type' : 'data', 'html' : urllib.quote( input.get_html( trans ) ) } ) + elif isinstance( input, SelectToolParameter ): + param_dict.update( { 'type' : 'select', 'html' : urllib.quote( input.get_html( trans ) ) } ) + elif isinstance( input, Conditional ): + # TODO. + pass + else: + param_dict.update( { 'type' : '??', 'init_value' : input.value, \ + 'html' : urllib.quote( input.get_html( trans ) ) } ) + inputs.append( param_dict ) + + tool_dict[ 'inputs' ] = inputs + + # Dictify outputs. + pass + + return tool_dict class DataSourceTool( Tool ): """ diff -r 84d49e39069d965a45097ade1b71a57cdc0a0386 -r f11e8aa26fcc88b9fa92e752000b092cfefce88c lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -6,7 +6,7 @@ RESTful controller for interactions with tools. """ - @web.json + @web.expose_api def index( self, trans, **kwds ): """ GET /api/tools: returns a list of tools defined by parameters @@ -22,11 +22,11 @@ # Create return value. return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) - @web.expose_api + @web.json def show( self, trans, id, **kwd ): """ GET /api/tools/{tool_id} Returns tool information, including parameters and inputs. """ - return self.app.toolbox.tools_by_id[ id ].to_dict( trans, all=True ) + return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True ) \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/272506e479f5/ changeset: 272506e479f5 user: jgoecks date: 2012-04-12 20:18:44 summary: Basic support for dynamically displaying tool forms. affected #: 7 files diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1632,7 +1632,7 @@ margin-top: 5px; } -.unified-panel-body > .toolMenu { +.unified-panel-body .toolMenu { padding: 10px; } @@ -1717,5 +1717,13 @@ padding:2px 10px; } +// ==== Integrated tool form styles + +.toolMenuAndView .toolForm +{ + float: left; + background-color: white; + margin: 10px; +} @import "base_sprites"; diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -713,7 +713,7 @@ pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} .toolMenuContainer{color:#303030;background:#dfe5f9;margin-top:5px;} -.unified-panel-body>.toolMenu{padding:10px;} +.unified-panel-body .toolMenu{padding:10px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionWrapper{margin-bottom:5px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} @@ -725,6 +725,7 @@ #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} #loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;background:url(largespinner.gif);} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} +.toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -8,7 +8,7 @@ * Simple base model for any visible element. Includes useful attributes and ability * to set and track visibility. */ -var BaseModel = Backbone.Model.extend({ +var BaseModel = Backbone.RelationalModel.extend({ defaults: { name: null, hidden: false @@ -35,9 +35,22 @@ defaults: { description: null, target: null, - params: [] + inputs: [] }, + relations: [ + { + type: Backbone.HasMany, + key: 'inputs', + relatedModel: 'ToolInput', + reverseRelation: { + key: 'tool' + } + } + ], + + urlRoot: galaxy_paths.attributes.root_path + 'api/tools', + apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); return this.is_visible(); @@ -45,6 +58,17 @@ }); /** + * A tool input. + */ +var ToolInput = Backbone.RelationalModel.extend({ + + initialize: function() { + this.attributes.html = unescape(this.attributes.html); + } + +}); + +/** * Wrap collection of tools for fast access/manipulation. */ var ToolCollection = Backbone.Collection.extend({ @@ -379,6 +403,10 @@ } }); +/** + * Tool panel view. Events triggered include: + * tool_link_click(click event, tool_model) + */ var ToolPanelView = Backbone.View.extend({ tagName: 'div', className: 'toolMenu', @@ -386,13 +414,8 @@ /** * Waits for collection to load and then renders. */ - initialize: function(options) { + initialize: function() { this.collection.tool_search.on("change:results", this.handle_search_results, this); - - this.tool_link_click_fn = null; - if (options && 'tool_link_click_fn' in options) { - this.tool_link_click_fn = options.tool_link_click_fn; - } }, render: function() { @@ -422,16 +445,15 @@ } }); - // Setup tool link click handling. - if (self.tool_link_click_fn) { - self.$el.find("a.tool-link").click(function() { - // Tool id is always the first class. - var tool_id = $(this).attr('class').split(/\s+/)[0]; + // Setup tool link click eventing. + self.$el.find("a.tool-link").click(function(e) { + // Tool id is always the first class. + var + tool_id = $(this).attr('class').split(/\s+/)[0], + tool = self.collection.tools.get(tool_id); - self.tool_link_click_fn(self.collection.tools.get(tool_id)); - return false; - }); - } + self.trigger("tool_link_click", e, tool); + }); return this; }, @@ -446,3 +468,62 @@ } } }); + +/** + * View for working with a tool: setting parameters and inputs and executing the tool. + */ +var ToolFormView = Backbone.View.extend({ + className: 'toolForm', + template: Handlebars.templates.tool_form, + + render: function() { + this.$el.children().remove(); + this.$el.append( this.template(this.model.toJSON()) ); + } +}); + + +/** + * Integrated tool menu + tool execution. + */ +var IntegratedToolMenuAndView = Backbone.View.extend({ + className: 'toolMenuAndView', + + initialize: function() { + this.tool_panel_view = new ToolPanelView({collection: this.collection}); + this.tool_form_view = new ToolFormView(); + }, + + render: function() { + // Render and append tool panel. + this.tool_panel_view.render(); + this.tool_panel_view.$el.css("float", "left"); + this.$el.append(this.tool_panel_view.$el); + + // Append tool form view. + this.tool_form_view.$el.hide(); + this.$el.append(this.tool_form_view.$el); + + // On tool link click, show tool. + var self = this; + this.tool_panel_view.on("tool_link_click", function(e, tool) { + // Prevents click from activating link: + e.preventDefault(); + // Show tool that was clicked on: + self.show_tool(tool); + }); + }, + + /** + * Fetch and display tool. + */ + show_tool: function(tool) { + var self = this; + tool.fetch().done( function() { + self.tool_form_view.model = tool; + self.tool_form_view.render(); + self.tool_form_view.$el.show(); + $('#left').width("650px"); + }); + } +}); \ No newline at end of file diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/scripts/handlebars/compiled/tool_form.js --- /dev/null +++ b/static/scripts/handlebars/compiled/tool_form.js @@ -0,0 +1,61 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_form'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, stack2, foundHelper, tmp1, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"form-row\">\n <label for=\""; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.label; + stack1 = foundHelper || depth0.label; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "label", { hash: {} }); } + buffer += escapeExpression(stack1) + ":</label>\n <div class=\"form-row-input\">\n "; + foundHelper = helpers.html; + stack1 = foundHelper || depth0.html; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "html", { hash: {} }); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "; + foundHelper = helpers.help; + stack1 = foundHelper || depth0.help; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + buffer += escapeExpression(stack1) + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n "; + return buffer;} + + buffer += "<div class=\"toolFormTitle\">"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + " (version "; + foundHelper = helpers.version; + stack1 = foundHelper || depth0.version; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "version", { hash: {} }); } + buffer += escapeExpression(stack1) + ")</div>\n <div class=\"toolFormBody\">\n "; + foundHelper = helpers.inputs; + stack1 = foundHelper || depth0.inputs; + stack2 = helpers.each; + tmp1 = self.program(1, program1, data); + tmp1.hash = {}; + tmp1.fn = tmp1; + tmp1.inverse = self.noop; + stack1 = stack2.call(depth0, stack1, tmp1); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"; + foundHelper = helpers.help; + stack1 = foundHelper || depth0.help; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + buffer += escapeExpression(stack1) + "</div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/scripts/handlebars/tool_form.handlebars --- /dev/null +++ b/static/scripts/handlebars/tool_form.handlebars @@ -0,0 +1,21 @@ +<div class="toolFormTitle">{{name}} (version {{version}})</div> + <div class="toolFormBody"> + {{#each inputs}} + <div class="form-row"> + <label for="{{name}}">{{label}}:</label> + <div class="form-row-input"> + {{{html}}} + </div> + <div class="toolParamHelp" style="clear: both;"> + {{help}} + </div> + <div style="clear: both;"></div> + </div> + {{/each}} + </div> + <div class="form-row form-actions"> + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> +</div> +<div class="toolHelp"> + <div class="toolHelpBody">{{help}}</div> +</div> \ No newline at end of file diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();b.append(f.$el)}}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool"}}],url:function(){return galaxy_paths.attributes.root_path+"tools/show?id="+this.id},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolInput=Backbone.RelationalModel.extend({});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolView=Backbone.View.extend({className:"toolForm",render:function(){var a=this}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection})},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(a){a.fetch().done(function(){console.log(a);var b=new ToolView({model:a});b.render();b.$el.css("float","left");this.$el.append(b.$el);$("#left").width("500px")})}}); \ No newline at end of file diff -r f11e8aa26fcc88b9fa92e752000b092cfefce88c -r 272506e479f54d41b345c373786c23cab57cc153 static/scripts/packed/handlebars/compiled/tool_form.js --- /dev/null +++ b/static/scripts/packed/handlebars/compiled/tool_form.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,p,e,n,m){e=e||f.helpers;var k="",c,r,j,i,q=this,g="function",o=e.helperMissing,h=void 0,l=this.escapeExpression;function d(v,u){var s="",t;s+='\n <div class="form-row">\n <label for="';j=e.name;t=j||v.name;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"name",{hash:{}})}}s+=l(t)+'">';j=e.label;t=j||v.label;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"label",{hash:{}})}}s+=l(t)+':</label>\n <div class="form-row-input">\n ';j=e.html;t=j||v.html;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"html",{hash:{}})}}if(t||t===0){s+=t}s+='\n </div>\n <div class="toolParamHelp" style="clear: both;">\n ';j=e.help;t=j||v.help;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"help",{hash:{}})}}s+=l(t)+'\n </div>\n <div style="clear: both;"></div>\n </div>\n ';return s}k+='<div class="toolFormTitle">';j=e.name;c=j||p.name;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"name",{hash:{}})}}k+=l(c)+" (version ";j=e.version;c=j||p.version;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"version",{hash:{}})}}k+=l(c)+')</div>\n <div class="toolFormBody">\n ';j=e.inputs;c=j||p.inputs;r=e.each;i=q.program(1,d,m);i.hash={};i.fn=i;i.inverse=q.noop;c=r.call(p,c,i);if(c||c===0){k+=c}k+='\n </div>\n <div class="form-row form-actions">\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n <div class="toolHelpBody">';j=e.help;c=j||p.help;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"help",{hash:{}})}}k+=l(c)+"</div>\n</div>";return k})})(); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/98c2b1689ab3/ changeset: 98c2b1689ab3 user: jgoecks date: 2012-04-12 20:21:35 summary: Change handlebars directory name to templates. affected #: 32 files diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compile_templates.py --- a/static/scripts/handlebars/compile_templates.py +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env python - -# Script requires handlebars compiler be installed; use node package manager -# to install handlebars. - -import sys - -from glob import glob -from subprocess import call -from shutil import copyfile -from os import path - -cmd = "handlebars %s -f compiled/%s.js" - -# If specific scripts specified on command line, just pack them, otherwise pack -# all. - -if len( sys.argv ) > 1: - to_pack = sys.argv[1:] -else: - to_pack = glob( "*.handlebars" ) - -for fname in to_pack: - fname_base = path.splitext( path.split( fname )[1] )[0] - print "%s --> compiled/%s.js" % ( fname, fname_base ) - out = call( cmd % ( fname, fname_base ), shell=True ) diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compiled/panel_label.js --- a/static/scripts/handlebars/compiled/panel_label.js +++ /dev/null @@ -1,15 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['panel_label'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - - - buffer += "<span>"; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + "</span>"; - return buffer;}); -})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compiled/panel_section.js --- a/static/scripts/handlebars/compiled/panel_section.js +++ /dev/null @@ -1,25 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['panel_section'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - - - buffer += "<div class=\"toolSectionTitle\" id=\"title_"; - foundHelper = helpers.id; - stack1 = foundHelper || depth0.id; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } - buffer += escapeExpression(stack1) + "\">\n <a href=\"#\"><span>"; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + "</span></a>\n</div>\n<div id=\""; - foundHelper = helpers.id; - stack1 = foundHelper || depth0.id; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } - buffer += escapeExpression(stack1) + "\" class=\"toolSectionBody\" style=\"display: none; \">\n <div class=\"toolSectionBg\"></div>\n<div>"; - return buffer;}); -})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compiled/tool_form.js --- a/static/scripts/handlebars/compiled/tool_form.js +++ /dev/null @@ -1,61 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_form'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, stack2, foundHelper, tmp1, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"form-row\">\n <label for=\""; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.label; - stack1 = foundHelper || depth0.label; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "label", { hash: {} }); } - buffer += escapeExpression(stack1) + ":</label>\n <div class=\"form-row-input\">\n "; - foundHelper = helpers.html; - stack1 = foundHelper || depth0.html; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "html", { hash: {} }); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "; - foundHelper = helpers.help; - stack1 = foundHelper || depth0.help; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } - buffer += escapeExpression(stack1) + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n "; - return buffer;} - - buffer += "<div class=\"toolFormTitle\">"; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + " (version "; - foundHelper = helpers.version; - stack1 = foundHelper || depth0.version; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "version", { hash: {} }); } - buffer += escapeExpression(stack1) + ")</div>\n <div class=\"toolFormBody\">\n "; - foundHelper = helpers.inputs; - stack1 = foundHelper || depth0.inputs; - stack2 = helpers.each; - tmp1 = self.program(1, program1, data); - tmp1.hash = {}; - tmp1.fn = tmp1; - tmp1.inverse = self.noop; - stack1 = stack2.call(depth0, stack1, tmp1); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"; - foundHelper = helpers.help; - stack1 = foundHelper || depth0.help; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } - buffer += escapeExpression(stack1) + "</div>\n</div>"; - return buffer;}); -})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compiled/tool_link.js --- a/static/scripts/handlebars/compiled/tool_link.js +++ /dev/null @@ -1,40 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_link'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - - - buffer += "<a class=\""; - foundHelper = helpers.id; - stack1 = foundHelper || depth0.id; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } - buffer += escapeExpression(stack1) + " tool-link\" href=\""; - foundHelper = helpers.link; - stack1 = foundHelper || depth0.link; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "link", { hash: {} }); } - buffer += escapeExpression(stack1) + "\" target=\""; - foundHelper = helpers.target; - stack1 = foundHelper || depth0.target; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "target", { hash: {} }); } - buffer += escapeExpression(stack1) + "\" minsizehint=\""; - foundHelper = helpers.min_width; - stack1 = foundHelper || depth0.min_width; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "min_width", { hash: {} }); } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + "</a> "; - foundHelper = helpers.description; - stack1 = foundHelper || depth0.description; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "description", { hash: {} }); } - buffer += escapeExpression(stack1); - return buffer;}); -})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/compiled/tool_search.js --- a/static/scripts/handlebars/compiled/tool_search.js +++ /dev/null @@ -1,15 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_search'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - - - buffer += "<input type=\"text\" name=\"query\" value=\"search tools\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<img src=\""; - foundHelper = helpers.spinner_url; - stack1 = foundHelper || depth0.spinner_url; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "spinner_url", { hash: {} }); } - buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n"; - return buffer;}); -})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/panel_label.handlebars --- a/static/scripts/handlebars/panel_label.handlebars +++ /dev/null @@ -1,1 +0,0 @@ -<span>{{name}}</span> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/panel_section.handlebars --- a/static/scripts/handlebars/panel_section.handlebars +++ /dev/null @@ -1,6 +0,0 @@ -<div class="toolSectionTitle" id="title_{{id}}"> - <a href="#"><span>{{name}}</span></a> -</div> -<div id="{{id}}" class="toolSectionBody" style="display: none; "> - <div class="toolSectionBg"></div> -<div> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/tool_form.handlebars --- a/static/scripts/handlebars/tool_form.handlebars +++ /dev/null @@ -1,21 +0,0 @@ -<div class="toolFormTitle">{{name}} (version {{version}})</div> - <div class="toolFormBody"> - {{#each inputs}} - <div class="form-row"> - <label for="{{name}}">{{label}}:</label> - <div class="form-row-input"> - {{{html}}} - </div> - <div class="toolParamHelp" style="clear: both;"> - {{help}} - </div> - <div style="clear: both;"></div> - </div> - {{/each}} - </div> - <div class="form-row form-actions"> - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> -</div> -<div class="toolHelp"> - <div class="toolHelpBody">{{help}}</div> -</div> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/tool_link.handlebars --- a/static/scripts/handlebars/tool_link.handlebars +++ /dev/null @@ -1,1 +0,0 @@ -<a class="{{id}} tool-link" href="{{link}}" target="{{target}}" minsizehint="{{min_width}}">{{name}}</a> {{description}} \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/handlebars/tool_search.handlebars --- a/static/scripts/handlebars/tool_search.handlebars +++ /dev/null @@ -1,2 +0,0 @@ -<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/handlebars/compiled/panel_label.js --- a/static/scripts/packed/handlebars/compiled/panel_label.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_label=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+="<span>";h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</span>";return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/handlebars/compiled/panel_section.js --- a/static/scripts/packed/handlebars/compiled/panel_section.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<div class="toolSectionTitle" id="title_';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'">\n <a href="#"><span>';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+'</span></a>\n</div>\n<div id="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'" class="toolSectionBody" style="display: none; ">\n <div class="toolSectionBg"></div>\n<div>';return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/handlebars/compiled/tool_form.js --- a/static/scripts/packed/handlebars/compiled/tool_form.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,p,e,n,m){e=e||f.helpers;var k="",c,r,j,i,q=this,g="function",o=e.helperMissing,h=void 0,l=this.escapeExpression;function d(v,u){var s="",t;s+='\n <div class="form-row">\n <label for="';j=e.name;t=j||v.name;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"name",{hash:{}})}}s+=l(t)+'">';j=e.label;t=j||v.label;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"label",{hash:{}})}}s+=l(t)+':</label>\n <div class="form-row-input">\n ';j=e.html;t=j||v.html;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"html",{hash:{}})}}if(t||t===0){s+=t}s+='\n </div>\n <div class="toolParamHelp" style="clear: both;">\n ';j=e.help;t=j||v.help;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"help",{hash:{}})}}s+=l(t)+'\n </div>\n <div style="clear: both;"></div>\n </div>\n ';return s}k+='<div class="toolFormTitle">';j=e.name;c=j||p.name;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"name",{hash:{}})}}k+=l(c)+" (version ";j=e.version;c=j||p.version;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"version",{hash:{}})}}k+=l(c)+')</div>\n <div class="toolFormBody">\n ';j=e.inputs;c=j||p.inputs;r=e.each;i=q.program(1,d,m);i.hash={};i.fn=i;i.inverse=q.noop;c=r.call(p,c,i);if(c||c===0){k+=c}k+='\n </div>\n <div class="form-row form-actions">\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n <div class="toolHelpBody">';j=e.help;c=j||p.help;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"help",{hash:{}})}}k+=l(c)+"</div>\n</div>";return k})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/handlebars/compiled/tool_link.js --- a/static/scripts/packed/handlebars/compiled/tool_link.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<a class="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+' tool-link" href="';h=d.link;c=h||n.link;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"link",{hash:{}})}}i+=j(c)+'" target="';h=d.target;c=h||n.target;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"target",{hash:{}})}}i+=j(c)+'" minsizehint="';h=d.min_width;c=h||n.min_width;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"min_width",{hash:{}})}}i+=j(c)+'">';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</a> ";h=d.description;c=h||n.description;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"description",{hash:{}})}}i+=j(c);return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/handlebars/compiled/tool_search.js --- a/static/scripts/packed/handlebars/compiled/tool_search.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<img src="';h=d.spinner_url;c=h||n.spinner_url;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"spinner_url",{hash:{}})}}i+=j(c)+'" id="search-spinner" class="search-spinner"/>\n';return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/templates/compiled/panel_label.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/panel_label.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_label=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+="<span>";h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</span>";return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/templates/compiled/panel_section.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/panel_section.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<div class="toolSectionTitle" id="title_';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'">\n <a href="#"><span>';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+'</span></a>\n</div>\n<div id="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'" class="toolSectionBody" style="display: none; ">\n <div class="toolSectionBg"></div>\n<div>';return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/templates/compiled/tool_form.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/tool_form.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,p,e,n,m){e=e||f.helpers;var k="",c,r,j,i,q=this,g="function",o=e.helperMissing,h=void 0,l=this.escapeExpression;function d(v,u){var s="",t;s+='\n <div class="form-row">\n <label for="';j=e.name;t=j||v.name;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"name",{hash:{}})}}s+=l(t)+'">';j=e.label;t=j||v.label;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"label",{hash:{}})}}s+=l(t)+':</label>\n <div class="form-row-input">\n ';j=e.html;t=j||v.html;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"html",{hash:{}})}}if(t||t===0){s+=t}s+='\n </div>\n <div class="toolParamHelp" style="clear: both;">\n ';j=e.help;t=j||v.help;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"help",{hash:{}})}}s+=l(t)+'\n </div>\n <div style="clear: both;"></div>\n </div>\n ';return s}k+='<div class="toolFormTitle">';j=e.name;c=j||p.name;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"name",{hash:{}})}}k+=l(c)+" (version ";j=e.version;c=j||p.version;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"version",{hash:{}})}}k+=l(c)+')</div>\n <div class="toolFormBody">\n ';j=e.inputs;c=j||p.inputs;r=e.each;i=q.program(1,d,m);i.hash={};i.fn=i;i.inverse=q.noop;c=r.call(p,c,i);if(c||c===0){k+=c}k+='\n </div>\n <div class="form-row form-actions">\n <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n <div class="toolHelpBody">';j=e.help;c=j||p.help;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"help",{hash:{}})}}k+=l(c)+"</div>\n</div>";return k})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/templates/compiled/tool_link.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/tool_link.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<a class="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+' tool-link" href="';h=d.link;c=h||n.link;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"link",{hash:{}})}}i+=j(c)+'" target="';h=d.target;c=h||n.target;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"target",{hash:{}})}}i+=j(c)+'" minsizehint="';h=d.min_width;c=h||n.min_width;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"min_width",{hash:{}})}}i+=j(c)+'">';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</a> ";h=d.description;c=h||n.description;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"description",{hash:{}})}}i+=j(c);return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/packed/templates/compiled/tool_search.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/tool_search.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<img src="';h=d.spinner_url;c=h||n.spinner_url;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"spinner_url",{hash:{}})}}i+=j(c)+'" id="search-spinner" class="search-spinner"/>\n';return i})})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compile_templates.py --- /dev/null +++ b/static/scripts/templates/compile_templates.py @@ -0,0 +1,26 @@ +#!/usr/bin/env python + +# Script requires handlebars compiler be installed; use node package manager +# to install handlebars. + +import sys + +from glob import glob +from subprocess import call +from shutil import copyfile +from os import path + +cmd = "handlebars %s -f compiled/%s.js" + +# If specific scripts specified on command line, just pack them, otherwise pack +# all. + +if len( sys.argv ) > 1: + to_pack = sys.argv[1:] +else: + to_pack = glob( "*.handlebars" ) + +for fname in to_pack: + fname_base = path.splitext( path.split( fname )[1] )[0] + print "%s --> compiled/%s.js" % ( fname, fname_base ) + out = call( cmd % ( fname, fname_base ), shell=True ) diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compiled/panel_label.js --- /dev/null +++ b/static/scripts/templates/compiled/panel_label.js @@ -0,0 +1,15 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['panel_label'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<span>"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</span>"; + return buffer;}); +})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compiled/panel_section.js --- /dev/null +++ b/static/scripts/templates/compiled/panel_section.js @@ -0,0 +1,25 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['panel_section'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<div class=\"toolSectionTitle\" id=\"title_"; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">\n <a href=\"#\"><span>"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</span></a>\n</div>\n<div id=\""; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" class=\"toolSectionBody\" style=\"display: none; \">\n <div class=\"toolSectionBg\"></div>\n<div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compiled/tool_form.js --- /dev/null +++ b/static/scripts/templates/compiled/tool_form.js @@ -0,0 +1,61 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_form'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, stack2, foundHelper, tmp1, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"form-row\">\n <label for=\""; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.label; + stack1 = foundHelper || depth0.label; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "label", { hash: {} }); } + buffer += escapeExpression(stack1) + ":</label>\n <div class=\"form-row-input\">\n "; + foundHelper = helpers.html; + stack1 = foundHelper || depth0.html; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "html", { hash: {} }); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "; + foundHelper = helpers.help; + stack1 = foundHelper || depth0.help; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + buffer += escapeExpression(stack1) + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n "; + return buffer;} + + buffer += "<div class=\"toolFormTitle\">"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + " (version "; + foundHelper = helpers.version; + stack1 = foundHelper || depth0.version; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "version", { hash: {} }); } + buffer += escapeExpression(stack1) + ")</div>\n <div class=\"toolFormBody\">\n "; + foundHelper = helpers.inputs; + stack1 = foundHelper || depth0.inputs; + stack2 = helpers.each; + tmp1 = self.program(1, program1, data); + tmp1.hash = {}; + tmp1.fn = tmp1; + tmp1.inverse = self.noop; + stack1 = stack2.call(depth0, stack1, tmp1); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"; + foundHelper = helpers.help; + stack1 = foundHelper || depth0.help; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + buffer += escapeExpression(stack1) + "</div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compiled/tool_link.js --- /dev/null +++ b/static/scripts/templates/compiled/tool_link.js @@ -0,0 +1,40 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_link'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<a class=\""; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + " tool-link\" href=\""; + foundHelper = helpers.link; + stack1 = foundHelper || depth0.link; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "link", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" target=\""; + foundHelper = helpers.target; + stack1 = foundHelper || depth0.target; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "target", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" minsizehint=\""; + foundHelper = helpers.min_width; + stack1 = foundHelper || depth0.min_width; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "min_width", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</a> "; + foundHelper = helpers.description; + stack1 = foundHelper || depth0.description; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "description", { hash: {} }); } + buffer += escapeExpression(stack1); + return buffer;}); +})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/compiled/tool_search.js --- /dev/null +++ b/static/scripts/templates/compiled/tool_search.js @@ -0,0 +1,15 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_search'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<input type=\"text\" name=\"query\" value=\"search tools\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<img src=\""; + foundHelper = helpers.spinner_url; + stack1 = foundHelper || depth0.spinner_url; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "spinner_url", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n"; + return buffer;}); +})(); \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/panel_label.handlebars --- /dev/null +++ b/static/scripts/templates/panel_label.handlebars @@ -0,0 +1,1 @@ +<span>{{name}}</span> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/panel_section.handlebars --- /dev/null +++ b/static/scripts/templates/panel_section.handlebars @@ -0,0 +1,6 @@ +<div class="toolSectionTitle" id="title_{{id}}"> + <a href="#"><span>{{name}}</span></a> +</div> +<div id="{{id}}" class="toolSectionBody" style="display: none; "> + <div class="toolSectionBg"></div> +<div> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/tool_form.handlebars --- /dev/null +++ b/static/scripts/templates/tool_form.handlebars @@ -0,0 +1,21 @@ +<div class="toolFormTitle">{{name}} (version {{version}})</div> + <div class="toolFormBody"> + {{#each inputs}} + <div class="form-row"> + <label for="{{name}}">{{label}}:</label> + <div class="form-row-input"> + {{{html}}} + </div> + <div class="toolParamHelp" style="clear: both;"> + {{help}} + </div> + <div style="clear: both;"></div> + </div> + {{/each}} + </div> + <div class="form-row form-actions"> + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> +</div> +<div class="toolHelp"> + <div class="toolHelpBody">{{help}}</div> +</div> \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/tool_link.handlebars --- /dev/null +++ b/static/scripts/templates/tool_link.handlebars @@ -0,0 +1,1 @@ +<a class="{{id}} tool-link" href="{{link}}" target="{{target}}" minsizehint="{{min_width}}">{{name}}</a> {{description}} \ No newline at end of file diff -r 272506e479f54d41b345c373786c23cab57cc153 -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d static/scripts/templates/tool_search.handlebars --- /dev/null +++ b/static/scripts/templates/tool_search.handlebars @@ -0,0 +1,2 @@ +<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> https://bitbucket.org/galaxy/galaxy-central/changeset/e7dc2ec85d1b/ changeset: e7dc2ec85d1b user: jgoecks date: 2012-04-12 20:29:36 summary: Change name of directory with backbone code to mvc. affected #: 8 files diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ /dev/null @@ -1,529 +0,0 @@ -/** - * Model classes for Galaxy tools and tool panel. Models have no references to views, - * instead using events to indicate state changes; this is advantageous because - * multiple views can use the same object and models can be used without views. - */ - -/** - * Simple base model for any visible element. Includes useful attributes and ability - * to set and track visibility. - */ -var BaseModel = Backbone.RelationalModel.extend({ - defaults: { - name: null, - hidden: false - }, - - show: function() { - this.set("hidden", false); - }, - - hide: function() { - this.set("hidden", true); - }, - - is_visible: function() { - return !this.attributes.hidden; - } -}); - -/** - * A Galaxy tool. - */ -var Tool = BaseModel.extend({ - // Default attributes. - defaults: { - description: null, - target: null, - inputs: [] - }, - - relations: [ - { - type: Backbone.HasMany, - key: 'inputs', - relatedModel: 'ToolInput', - reverseRelation: { - key: 'tool' - } - } - ], - - urlRoot: galaxy_paths.attributes.root_path + 'api/tools', - - apply_search_results: function(results) { - ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); - return this.is_visible(); - } -}); - -/** - * A tool input. - */ -var ToolInput = Backbone.RelationalModel.extend({ - - initialize: function() { - this.attributes.html = unescape(this.attributes.html); - } - -}); - -/** - * Wrap collection of tools for fast access/manipulation. - */ -var ToolCollection = Backbone.Collection.extend({ - model: Tool -}); - -/** - * Label or section header in tool panel. - */ -var ToolPanelLabel = BaseModel.extend({}); - -/** - * Section of tool panel with elements (labels and tools). - */ -var ToolPanelSection = BaseModel.extend({ - defaults: { - elems: [], - open: false - }, - - clear_search_results: function() { - _.each(this.attributes.elems, function(elt) { - elt.show(); - }); - - this.show(); - this.set("open", false); - }, - - apply_search_results: function(results) { - var all_hidden = true, - cur_label; - _.each(this.attributes.elems, function(elt) { - if (elt instanceof ToolPanelLabel) { - cur_label = elt; - cur_label.hide(); - } - else if (elt instanceof Tool) { - if (elt.apply_search_results(results)) { - all_hidden = false; - if (cur_label) { - cur_label.show(); - } - } - } - }); - - if (all_hidden) { - this.hide(); - } - else { - this.show(); - this.set("open", true); - } - } -}); - -/** - * Tool search that updates results when query is changed. Result value of null - * indicates that query was not run; if not null, results are from search using - * query. - */ -var ToolSearch = BaseModel.extend({ - defaults: { - spinner_url: "", - search_url: "", - visible: true, - query: "", - results: null - }, - - initialize: function() { - this.on("change:query", this.do_search); - }, - - /** - * Do the search and update the results. - */ - do_search: function() { - var query = this.attributes.query; - - // If query is too short, do not search. - if (query.length < 3) { - this.set("results", null); - return; - } - - // Do search via AJAX. - var q = query + '*'; - // Stop previous ajax-request - if (this.timer) { - clearTimeout(this.timer); - } - // Start a new ajax-request in X ms - $("#search-spinner").show(); - var self = this; - this.timer = setTimeout(function () { - $.get(self.attributes.search_url, { query: q }, function (data) { - self.set("results", data); - $("#search-spinner").hide(); - }, "json" ); - }, 200 ); - } -}); - -/** - * A collection of ToolPanelSections, Tools, and ToolPanelLabels. Collection - * applies search results as they become available. - */ -var ToolPanel = Backbone.Collection.extend({ - url: "/tools", - tools: new ToolCollection(), - - parse: function(response) { - // Recursive function to parse tool panel elements. - var parse_elt = function(elt_dict) { - var type = elt_dict.type; - if (type === 'tool') { - return new Tool(elt_dict); - } - else if (type === 'section') { - // Parse elements. - var elems = _.map(elt_dict.elems, parse_elt); - elt_dict.elems = elems; - return new ToolPanelSection(elt_dict); - } - else if (type === 'label') { - return new ToolPanelLabel(elt_dict); - } - }; - - return _.map(response, parse_elt); - }, - - initialize: function(options) { - this.tool_search = options.tool_search; - this.tool_search.on("change:results", this.apply_search_results, this); - this.on("reset", this.populate_tools, this); - }, - - /** - * Populate tool collection from panel elements. - */ - populate_tools: function() { - var self = this; - self.tools = new ToolCollection(); - this.each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { - _.each(panel_elt.attributes.elems, function (section_elt) { - if (section_elt instanceof Tool) { - self.tools.push(section_elt); - } - }); - } - else if (panel_elt instanceof Tool) { - self.tools.push(panel_elt); - } - }); - }, - - clear_search_results: function() { - this.each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { - panel_elt.clear_search_results(); - } - else { - // Label or tool, so just show. - panel_elt.show(); - } - }); - }, - - apply_search_results: function() { - var results = this.tool_search.attributes.results; - if (results === null) { - this.clear_search_results(); - return; - } - - var cur_label = null; - this.each(function(panel_elt) { - if (panel_elt instanceof ToolPanelLabel) { - cur_label = panel_elt; - cur_label.hide(); - } - else if (panel_elt instanceof Tool) { - if (panel_elt.apply_search_results(results)) { - if (cur_label) { - cur_label.show(); - } - } - } - else { - // Starting new section, so clear current label. - cur_label = null; - panel_elt.apply_search_results(results); - } - }); - } -}); - -/** - * View classes for Galaxy tools and tool panel. - * - * Views use precompiled Handlebars templates for rendering. Views update as needed - * based on (a) model/collection events and (b) user interactions; in this sense, - * they are controllers are well and the HTML is the real view in the MVC architecture. - */ - -/** - * Base view that handles visibility based on model's hidden attribute. - */ -var BaseView = Backbone.View.extend({ - initialize: function() { - this.model.on("change:hidden", this.update_visible, this); - this.update_visible(); - }, - update_visible: function() { - ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); - } -}); - -/** - * Link to a tool. - */ -var ToolLinkView = BaseView.extend({ - tagName: 'div', - template: Handlebars.templates.tool_link, - - render: function() { - this.$el.append( this.template(this.model.toJSON()) ); - return this; - } -}); - -/** - * Panel label/section header. - */ -var ToolPanelLabelView = BaseView.extend({ - tagName: 'div', - className: 'toolPanelLabel', - template: Handlebars.templates.panel_label, - - render: function() { - this.$el.append( this.template(this.model.toJSON()) ); - return this; - }, -}); - -/** - * Panel section. - */ -var ToolPanelSectionView = BaseView.extend({ - tagName: 'div', - className: 'toolSectionWrapper', - template: Handlebars.templates.panel_section, - initialize: function() { - BaseView.prototype.initialize.call(this); - this.model.on("change:open", this.update_open, this); - }, - render: function() { - // Build using template. - this.$el.append( this.template(this.model.toJSON()) ); - - // Add tools to section. - var section_body = this.$el.find(".toolSectionBody"); - _.each(this.model.attributes.elems, function(elt) { - if (elt instanceof Tool) { - var tool_view = new ToolLinkView({model: elt, className: "toolTitle"}); - tool_view.render(); - section_body.append(tool_view.$el); - } - else if (elt instanceof ToolPanelLabel) { - var label_view = new ToolPanelLabelView({model: elt}); - label_view.render(); - section_body.append(label_view.$el); - } - else { - // TODO: handle nested section bodies? - } - }); - return this; - }, - - events: { - 'click .toolSectionTitle > a': 'toggle' - }, - - /** - * Toggle visibility of tool section. - */ - toggle: function() { - this.model.set("open", !this.model.attributes.open); - }, - - /** - * Update whether section is open or close. - */ - update_open: function() { - (this.model.attributes.open ? - this.$el.children(".toolSectionBody").slideDown("fast") : - this.$el.children(".toolSectionBody").slideUp("fast") - ); - } -}); - -var ToolSearchView = Backbone.View.extend({ - tagName: 'div', - id: 'tool-search', - className: 'bar', - template: Handlebars.templates.tool_search, - - events: { - 'click': 'focus_and_select', - 'keyup :input': 'query_changed' - }, - - render: function() { - this.$el.append( this.template(this.model.toJSON()) ); - if (!this.model.is_visible()) { - this.$el.hide(); - } - return this; - }, - - focus_and_select: function() { - this.$el.find(":input").focus().select(); - }, - - query_changed: function() { - this.model.set("query", this.$el.find(":input").val()); - } -}); - -/** - * Tool panel view. Events triggered include: - * tool_link_click(click event, tool_model) - */ -var ToolPanelView = Backbone.View.extend({ - tagName: 'div', - className: 'toolMenu', - - /** - * Waits for collection to load and then renders. - */ - initialize: function() { - this.collection.tool_search.on("change:results", this.handle_search_results, this); - }, - - render: function() { - var self = this; - - // Render search. - var search_view = new ToolSearchView( {model: this.collection.tool_search} ); - search_view.render(); - self.$el.append(search_view.$el); - - // Render panel. - this.collection.each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { - var section_title_view = new ToolPanelSectionView({model: panel_elt}); - section_title_view.render(); - self.$el.append(section_title_view.$el); - } - else if (panel_elt instanceof Tool) { - var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); - tool_view.render(); - self.$el.append(tool_view.$el); - } - else if (panel_elt instanceof ToolPanelLabel) { - var label_view = new ToolPanelLabelView({model: panel_elt}); - label_view.render(); - self.$el.append(label_view.$el); - } - }); - - // Setup tool link click eventing. - self.$el.find("a.tool-link").click(function(e) { - // Tool id is always the first class. - var - tool_id = $(this).attr('class').split(/\s+/)[0], - tool = self.collection.tools.get(tool_id); - - self.trigger("tool_link_click", e, tool); - }); - - return this; - }, - - handle_search_results: function() { - var results = this.collection.tool_search.attributes.results; - if (results && results.length === 0) { - $("#search-no-results").show(); - } - else { - $("#search-no-results").hide(); - } - } -}); - -/** - * View for working with a tool: setting parameters and inputs and executing the tool. - */ -var ToolFormView = Backbone.View.extend({ - className: 'toolForm', - template: Handlebars.templates.tool_form, - - render: function() { - this.$el.children().remove(); - this.$el.append( this.template(this.model.toJSON()) ); - } -}); - - -/** - * Integrated tool menu + tool execution. - */ -var IntegratedToolMenuAndView = Backbone.View.extend({ - className: 'toolMenuAndView', - - initialize: function() { - this.tool_panel_view = new ToolPanelView({collection: this.collection}); - this.tool_form_view = new ToolFormView(); - }, - - render: function() { - // Render and append tool panel. - this.tool_panel_view.render(); - this.tool_panel_view.$el.css("float", "left"); - this.$el.append(this.tool_panel_view.$el); - - // Append tool form view. - this.tool_form_view.$el.hide(); - this.$el.append(this.tool_form_view.$el); - - // On tool link click, show tool. - var self = this; - this.tool_panel_view.on("tool_link_click", function(e, tool) { - // Prevents click from activating link: - e.preventDefault(); - // Show tool that was clicked on: - self.show_tool(tool); - }); - }, - - /** - * Fetch and display tool. - */ - show_tool: function(tool) { - var self = this; - tool.fetch().done( function() { - self.tool_form_view.model = tool; - self.tool_form_view.render(); - self.tool_form_view.$el.show(); - $('#left').width("650px"); - }); - } -}); \ No newline at end of file diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/backbone/ui.js --- a/static/scripts/backbone/ui.js +++ /dev/null @@ -1,65 +0,0 @@ -/** - * Utility models and views for Galaxy objects. - */ - -/** - * Necessary Galaxy paths. - */ -var GalaxyPaths = Backbone.Model.extend({ - defaults: { - root_path: "", - image_path: "" - } -}); - -/** - * Clickable button represented as an icon. - */ -var IconButton = Backbone.Model.extend({ - defaults: { - title: "", - icon_class: "", - on_click: null - } -}); - -var IconButtonCollection = Backbone.Collection.extend({ - model: IconButton -}); - -/** - * Menu with multiple icon buttons. Views are not needed nor used for individual buttons. - */ -var IconButtonMenuView = Backbone.View.extend({ - tagName: 'div', - - render: function() { - var self = this; - this.collection.each(function(button) { - // Create and add icon button to menu. - $("<a/>").attr('href', 'javascript:void(0)') - .attr('title', button.attributes.title) - .addClass('icon-button menu-button') - .addClass(button.attributes.icon_class) - .appendTo(self.$el) - .click(button.attributes.on_click); - }); - return this; - } -}); - -/** - * - */ -var Grid = Backbone.Collection.extend({ - -}); - -/** - * - */ -var GridView = Backbone.View.extend({ - -}); - - diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/mvc/tools.js --- /dev/null +++ b/static/scripts/mvc/tools.js @@ -0,0 +1,529 @@ +/** + * Model classes for Galaxy tools and tool panel. Models have no references to views, + * instead using events to indicate state changes; this is advantageous because + * multiple views can use the same object and models can be used without views. + */ + +/** + * Simple base model for any visible element. Includes useful attributes and ability + * to set and track visibility. + */ +var BaseModel = Backbone.RelationalModel.extend({ + defaults: { + name: null, + hidden: false + }, + + show: function() { + this.set("hidden", false); + }, + + hide: function() { + this.set("hidden", true); + }, + + is_visible: function() { + return !this.attributes.hidden; + } +}); + +/** + * A Galaxy tool. + */ +var Tool = BaseModel.extend({ + // Default attributes. + defaults: { + description: null, + target: null, + inputs: [] + }, + + relations: [ + { + type: Backbone.HasMany, + key: 'inputs', + relatedModel: 'ToolInput', + reverseRelation: { + key: 'tool' + } + } + ], + + urlRoot: galaxy_paths.attributes.root_path + 'api/tools', + + apply_search_results: function(results) { + ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); + return this.is_visible(); + } +}); + +/** + * A tool input. + */ +var ToolInput = Backbone.RelationalModel.extend({ + + initialize: function() { + this.attributes.html = unescape(this.attributes.html); + } + +}); + +/** + * Wrap collection of tools for fast access/manipulation. + */ +var ToolCollection = Backbone.Collection.extend({ + model: Tool +}); + +/** + * Label or section header in tool panel. + */ +var ToolPanelLabel = BaseModel.extend({}); + +/** + * Section of tool panel with elements (labels and tools). + */ +var ToolPanelSection = BaseModel.extend({ + defaults: { + elems: [], + open: false + }, + + clear_search_results: function() { + _.each(this.attributes.elems, function(elt) { + elt.show(); + }); + + this.show(); + this.set("open", false); + }, + + apply_search_results: function(results) { + var all_hidden = true, + cur_label; + _.each(this.attributes.elems, function(elt) { + if (elt instanceof ToolPanelLabel) { + cur_label = elt; + cur_label.hide(); + } + else if (elt instanceof Tool) { + if (elt.apply_search_results(results)) { + all_hidden = false; + if (cur_label) { + cur_label.show(); + } + } + } + }); + + if (all_hidden) { + this.hide(); + } + else { + this.show(); + this.set("open", true); + } + } +}); + +/** + * Tool search that updates results when query is changed. Result value of null + * indicates that query was not run; if not null, results are from search using + * query. + */ +var ToolSearch = BaseModel.extend({ + defaults: { + spinner_url: "", + search_url: "", + visible: true, + query: "", + results: null + }, + + initialize: function() { + this.on("change:query", this.do_search); + }, + + /** + * Do the search and update the results. + */ + do_search: function() { + var query = this.attributes.query; + + // If query is too short, do not search. + if (query.length < 3) { + this.set("results", null); + return; + } + + // Do search via AJAX. + var q = query + '*'; + // Stop previous ajax-request + if (this.timer) { + clearTimeout(this.timer); + } + // Start a new ajax-request in X ms + $("#search-spinner").show(); + var self = this; + this.timer = setTimeout(function () { + $.get(self.attributes.search_url, { query: q }, function (data) { + self.set("results", data); + $("#search-spinner").hide(); + }, "json" ); + }, 200 ); + } +}); + +/** + * A collection of ToolPanelSections, Tools, and ToolPanelLabels. Collection + * applies search results as they become available. + */ +var ToolPanel = Backbone.Collection.extend({ + url: "/tools", + tools: new ToolCollection(), + + parse: function(response) { + // Recursive function to parse tool panel elements. + var parse_elt = function(elt_dict) { + var type = elt_dict.type; + if (type === 'tool') { + return new Tool(elt_dict); + } + else if (type === 'section') { + // Parse elements. + var elems = _.map(elt_dict.elems, parse_elt); + elt_dict.elems = elems; + return new ToolPanelSection(elt_dict); + } + else if (type === 'label') { + return new ToolPanelLabel(elt_dict); + } + }; + + return _.map(response, parse_elt); + }, + + initialize: function(options) { + this.tool_search = options.tool_search; + this.tool_search.on("change:results", this.apply_search_results, this); + this.on("reset", this.populate_tools, this); + }, + + /** + * Populate tool collection from panel elements. + */ + populate_tools: function() { + var self = this; + self.tools = new ToolCollection(); + this.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + _.each(panel_elt.attributes.elems, function (section_elt) { + if (section_elt instanceof Tool) { + self.tools.push(section_elt); + } + }); + } + else if (panel_elt instanceof Tool) { + self.tools.push(panel_elt); + } + }); + }, + + clear_search_results: function() { + this.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + panel_elt.clear_search_results(); + } + else { + // Label or tool, so just show. + panel_elt.show(); + } + }); + }, + + apply_search_results: function() { + var results = this.tool_search.attributes.results; + if (results === null) { + this.clear_search_results(); + return; + } + + var cur_label = null; + this.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelLabel) { + cur_label = panel_elt; + cur_label.hide(); + } + else if (panel_elt instanceof Tool) { + if (panel_elt.apply_search_results(results)) { + if (cur_label) { + cur_label.show(); + } + } + } + else { + // Starting new section, so clear current label. + cur_label = null; + panel_elt.apply_search_results(results); + } + }); + } +}); + +/** + * View classes for Galaxy tools and tool panel. + * + * Views use precompiled Handlebars templates for rendering. Views update as needed + * based on (a) model/collection events and (b) user interactions; in this sense, + * they are controllers are well and the HTML is the real view in the MVC architecture. + */ + +/** + * Base view that handles visibility based on model's hidden attribute. + */ +var BaseView = Backbone.View.extend({ + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + this.update_visible(); + }, + update_visible: function() { + ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); + } +}); + +/** + * Link to a tool. + */ +var ToolLinkView = BaseView.extend({ + tagName: 'div', + template: Handlebars.templates.tool_link, + + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + return this; + } +}); + +/** + * Panel label/section header. + */ +var ToolPanelLabelView = BaseView.extend({ + tagName: 'div', + className: 'toolPanelLabel', + template: Handlebars.templates.panel_label, + + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + return this; + }, +}); + +/** + * Panel section. + */ +var ToolPanelSectionView = BaseView.extend({ + tagName: 'div', + className: 'toolSectionWrapper', + template: Handlebars.templates.panel_section, + initialize: function() { + BaseView.prototype.initialize.call(this); + this.model.on("change:open", this.update_open, this); + }, + render: function() { + // Build using template. + this.$el.append( this.template(this.model.toJSON()) ); + + // Add tools to section. + var section_body = this.$el.find(".toolSectionBody"); + _.each(this.model.attributes.elems, function(elt) { + if (elt instanceof Tool) { + var tool_view = new ToolLinkView({model: elt, className: "toolTitle"}); + tool_view.render(); + section_body.append(tool_view.$el); + } + else if (elt instanceof ToolPanelLabel) { + var label_view = new ToolPanelLabelView({model: elt}); + label_view.render(); + section_body.append(label_view.$el); + } + else { + // TODO: handle nested section bodies? + } + }); + return this; + }, + + events: { + 'click .toolSectionTitle > a': 'toggle' + }, + + /** + * Toggle visibility of tool section. + */ + toggle: function() { + this.model.set("open", !this.model.attributes.open); + }, + + /** + * Update whether section is open or close. + */ + update_open: function() { + (this.model.attributes.open ? + this.$el.children(".toolSectionBody").slideDown("fast") : + this.$el.children(".toolSectionBody").slideUp("fast") + ); + } +}); + +var ToolSearchView = Backbone.View.extend({ + tagName: 'div', + id: 'tool-search', + className: 'bar', + template: Handlebars.templates.tool_search, + + events: { + 'click': 'focus_and_select', + 'keyup :input': 'query_changed' + }, + + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + if (!this.model.is_visible()) { + this.$el.hide(); + } + return this; + }, + + focus_and_select: function() { + this.$el.find(":input").focus().select(); + }, + + query_changed: function() { + this.model.set("query", this.$el.find(":input").val()); + } +}); + +/** + * Tool panel view. Events triggered include: + * tool_link_click(click event, tool_model) + */ +var ToolPanelView = Backbone.View.extend({ + tagName: 'div', + className: 'toolMenu', + + /** + * Waits for collection to load and then renders. + */ + initialize: function() { + this.collection.tool_search.on("change:results", this.handle_search_results, this); + }, + + render: function() { + var self = this; + + // Render search. + var search_view = new ToolSearchView( {model: this.collection.tool_search} ); + search_view.render(); + self.$el.append(search_view.$el); + + // Render panel. + this.collection.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + var section_title_view = new ToolPanelSectionView({model: panel_elt}); + section_title_view.render(); + self.$el.append(section_title_view.$el); + } + else if (panel_elt instanceof Tool) { + var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); + tool_view.render(); + self.$el.append(tool_view.$el); + } + else if (panel_elt instanceof ToolPanelLabel) { + var label_view = new ToolPanelLabelView({model: panel_elt}); + label_view.render(); + self.$el.append(label_view.$el); + } + }); + + // Setup tool link click eventing. + self.$el.find("a.tool-link").click(function(e) { + // Tool id is always the first class. + var + tool_id = $(this).attr('class').split(/\s+/)[0], + tool = self.collection.tools.get(tool_id); + + self.trigger("tool_link_click", e, tool); + }); + + return this; + }, + + handle_search_results: function() { + var results = this.collection.tool_search.attributes.results; + if (results && results.length === 0) { + $("#search-no-results").show(); + } + else { + $("#search-no-results").hide(); + } + } +}); + +/** + * View for working with a tool: setting parameters and inputs and executing the tool. + */ +var ToolFormView = Backbone.View.extend({ + className: 'toolForm', + template: Handlebars.templates.tool_form, + + render: function() { + this.$el.children().remove(); + this.$el.append( this.template(this.model.toJSON()) ); + } +}); + + +/** + * Integrated tool menu + tool execution. + */ +var IntegratedToolMenuAndView = Backbone.View.extend({ + className: 'toolMenuAndView', + + initialize: function() { + this.tool_panel_view = new ToolPanelView({collection: this.collection}); + this.tool_form_view = new ToolFormView(); + }, + + render: function() { + // Render and append tool panel. + this.tool_panel_view.render(); + this.tool_panel_view.$el.css("float", "left"); + this.$el.append(this.tool_panel_view.$el); + + // Append tool form view. + this.tool_form_view.$el.hide(); + this.$el.append(this.tool_form_view.$el); + + // On tool link click, show tool. + var self = this; + this.tool_panel_view.on("tool_link_click", function(e, tool) { + // Prevents click from activating link: + e.preventDefault(); + // Show tool that was clicked on: + self.show_tool(tool); + }); + }, + + /** + * Fetch and display tool. + */ + show_tool: function(tool) { + var self = this; + tool.fetch().done( function() { + self.tool_form_view.model = tool; + self.tool_form_view.render(); + self.tool_form_view.$el.show(); + $('#left').width("650px"); + }); + } +}); \ No newline at end of file diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/mvc/ui.js --- /dev/null +++ b/static/scripts/mvc/ui.js @@ -0,0 +1,65 @@ +/** + * Utility models and views for Galaxy objects. + */ + +/** + * Necessary Galaxy paths. + */ +var GalaxyPaths = Backbone.Model.extend({ + defaults: { + root_path: "", + image_path: "" + } +}); + +/** + * Clickable button represented as an icon. + */ +var IconButton = Backbone.Model.extend({ + defaults: { + title: "", + icon_class: "", + on_click: null + } +}); + +var IconButtonCollection = Backbone.Collection.extend({ + model: IconButton +}); + +/** + * Menu with multiple icon buttons. Views are not needed nor used for individual buttons. + */ +var IconButtonMenuView = Backbone.View.extend({ + tagName: 'div', + + render: function() { + var self = this; + this.collection.each(function(button) { + // Create and add icon button to menu. + $("<a/>").attr('href', 'javascript:void(0)') + .attr('title', button.attributes.title) + .addClass('icon-button menu-button') + .addClass(button.attributes.icon_class) + .appendTo(self.$el) + .click(button.attributes.on_click); + }); + return this; + } +}); + +/** + * + */ +var Grid = Backbone.Collection.extend({ + +}); + +/** + * + */ +var GridView = Backbone.View.extend({ + +}); + + diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ /dev/null @@ -1,1 +0,0 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool"}}],url:function(){return galaxy_paths.attributes.root_path+"tools/show?id="+this.id},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolInput=Backbone.RelationalModel.extend({});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolView=Backbone.View.extend({className:"toolForm",render:function(){var a=this}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection})},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(a){a.fetch().done(function(){console.log(a);var b=new ToolView({model:a});b.render();b.$el.css("float","left");this.$el.append(b.$el);$("#left").width("500px")})}}); \ No newline at end of file diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/packed/backbone/ui.js --- a/static/scripts/packed/backbone/ui.js +++ /dev/null @@ -1,1 +0,0 @@ -var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/packed/mvc/tools.js --- /dev/null +++ b/static/scripts/packed/mvc/tools.js @@ -0,0 +1,1 @@ +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool"}}],url:function(){return galaxy_paths.attributes.root_path+"tools/show?id="+this.id},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolInput=Backbone.RelationalModel.extend({});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolView=Backbone.View.extend({className:"toolForm",render:function(){var a=this}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection})},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(a){a.fetch().done(function(){console.log(a);var b=new ToolView({model:a});b.render();b.$el.css("float","left");this.$el.append(b.$el);$("#left").width("500px")})}}); \ No newline at end of file diff -r 98c2b1689ab32e5f15aa57906d95f1753c593c3d -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f static/scripts/packed/mvc/ui.js --- /dev/null +++ b/static/scripts/packed/mvc/ui.js @@ -0,0 +1,1 @@ +var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/98213ceeac03/ changeset: 98213ceeac03 user: jgoecks date: 2012-04-12 21:44:12 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 4 files diff -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f -r 98213ceeac03f0089b23ba64500802d69f3e77bb lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -250,7 +250,7 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = data.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) + trans.response.headers["Content-Disposition"] = 'attachment; filename="GalaxyHistoryItem-%s-[%s]%s"' % (data.hid, fname, toext) trans.log_event( "Display dataset id: %s" % str(id) ) try: return open( data.file_name ) diff -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f -r 98213ceeac03f0089b23ba64500802d69f3e77bb lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1109,7 +1109,7 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' sname = stored.name sname = ''.join(c in valid_chars and c or '_' for c in sname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname ) + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy-Workflow-%s.ga"' % ( sname ) trans.response.set_content_type( 'application/galaxy-archive' ) return stored_dict @web.expose diff -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f -r 98213ceeac03f0089b23ba64500802d69f3e77bb static/scripts/templates/compiled/panel_section.js --- a/static/scripts/templates/compiled/panel_section.js +++ b/static/scripts/templates/compiled/panel_section.js @@ -10,7 +10,7 @@ stack1 = foundHelper || depth0.id; if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } - buffer += escapeExpression(stack1) + "\">\n <a href=\"#\"><span>"; + buffer += escapeExpression(stack1) + "\">\n <a href=\"javascript:void(0)\"><span>"; foundHelper = helpers.name; stack1 = foundHelper || depth0.name; if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } diff -r e7dc2ec85d1ba124bd7f4558b3c5c89b56d55a0f -r 98213ceeac03f0089b23ba64500802d69f3e77bb static/scripts/templates/panel_section.handlebars --- a/static/scripts/templates/panel_section.handlebars +++ b/static/scripts/templates/panel_section.handlebars @@ -1,5 +1,5 @@ <div class="toolSectionTitle" id="title_{{id}}"> - <a href="#"><span>{{name}}</span></a> + <a href="javascript:void(0)"><span>{{name}}</span></a></div><div id="{{id}}" class="toolSectionBody" style="display: none; "><div class="toolSectionBg"></div> https://bitbucket.org/galaxy/galaxy-central/changeset/398905e25268/ changeset: 398905e25268 user: jgoecks date: 2012-04-13 16:04:42 summary: Update templates to reflect changes in javascript directories organization. affected #: 4 files diff -r 98213ceeac03f0089b23ba64500802d69f3e77bb -r 398905e25268a18e53eb2a01f9eb504020ece352 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -61,12 +61,12 @@ """ return js_helper( '/static/scripts/', *args ) -def handlebars( *args ): +def templates( *args ): """ Take a list of template names (no extension) and return appropriate string of script tags. """ - return js_helper( '/static/scripts/handlebars/compiled/', *args ) + return js_helper( '/static/scripts/templates/compiled/', *args ) # Hashes diff -r 98213ceeac03f0089b23ba64500802d69f3e77bb -r 398905e25268a18e53eb2a01f9eb504020ece352 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -26,7 +26,7 @@ ##  - ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/backbone-relational", "libs/handlebars.runtime", "backbone/ui" )} + ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )} <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 98213ceeac03f0089b23ba64500802d69f3e77bb -r 398905e25268a18e53eb2a01f9eb504020ece352 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -47,7 +47,7 @@  - ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/backbone-relational', 'libs/handlebars.runtime', 'backbone/ui' )} + ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )} <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 98213ceeac03f0089b23ba64500802d69f3e77bb -r 398905e25268a18e53eb2a01f9eb504020ece352 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -16,8 +16,8 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.handlebars( "tool_link", "panel_label", "panel_section", "tool_search" )} - ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "backbone/tools" )} + ${h.templates( "tool_link", "panel_label", "panel_section", "tool_search" )} + ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "mvc/tools" )} <% # Set up for creating tool panel. https://bitbucket.org/galaxy/galaxy-central/changeset/afd1b16d7ec5/ changeset: afd1b16d7ec5 user: jgoecks date: 2012-04-13 16:05:24 summary: Merge affected #: 1 file diff -r 398905e25268a18e53eb2a01f9eb504020ece352 -r afd1b16d7ec5d86dbe4f4a8d8636ec1d82d49f98 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -60,8 +60,6 @@ auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) action = 'login' - if not redirect: - redirect = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) if openid_url: openid_provider_obj = trans.app.openid_providers.new_provider_from_identifier( openid_url ) @@ -113,7 +111,7 @@ consumer = trans.app.openid_manager.get_consumer( trans ) info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() - redirect = kwd.get( 'redirect', url_for( '/' ) ) + redirect = kwd.get( 'redirect', '' ) openid_provider = kwd.get( 'openid_provider', None ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) @@ -163,6 +161,8 @@ openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + if redirect and status != "error": + return trans.response.send_redirect( redirect ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -173,6 +173,8 @@ trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) + if not redirect: + redirect = url_for( '/' ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -252,14 +254,19 @@ message = '%s<li><a href="%s" target="_blank">%s</a></li>' % ( message, url_for( controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True ), openid.name ) message = "%s</ul>" % ( message ) return trans.response.send_redirect( url_for( controller='user', - action='openid_manage', - use_panels=True, - redirect=redirect, - message=message, - status='info' ) ) - if not redirect: - redirect = url_for( '/' ) - return trans.response.send_redirect( redirect ) + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) + if redirect: + return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -304,9 +311,14 @@ redirect=redirect, message=message, status='info' ) ) - if not redirect: - redirect = url_for( '/' ) - return trans.response.send_redirect( redirect ) + if redirect: + return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) else: message = error status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Minor tweeks for redirect flow during OpenID process.
by Bitbucket 13 Apr '12

13 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f6e790d94282/ changeset: f6e790d94282 user: dan date: 2012-04-13 15:57:08 summary: Minor tweeks for redirect flow during OpenID process. affected #: 1 file diff -r a30f98b4b463f32a133f7a42d36411f0f9e63658 -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -60,8 +60,6 @@ auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) action = 'login' - if not redirect: - redirect = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) if openid_url: openid_provider_obj = trans.app.openid_providers.new_provider_from_identifier( openid_url ) @@ -113,7 +111,7 @@ consumer = trans.app.openid_manager.get_consumer( trans ) info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() - redirect = kwd.get( 'redirect', url_for( '/' ) ) + redirect = kwd.get( 'redirect', '' ) openid_provider = kwd.get( 'openid_provider', None ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) @@ -163,6 +161,8 @@ openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + if redirect and status != "error": + return trans.response.send_redirect( redirect ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -173,6 +173,8 @@ trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) + if not redirect: + redirect = url_for( '/' ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -252,14 +254,19 @@ message = '%s<li><a href="%s" target="_blank">%s</a></li>' % ( message, url_for( controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True ), openid.name ) message = "%s</ul>" % ( message ) return trans.response.send_redirect( url_for( controller='user', - action='openid_manage', - use_panels=True, - redirect=redirect, - message=message, - status='info' ) ) - if not redirect: - redirect = url_for( '/' ) - return trans.response.send_redirect( redirect ) + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) + if redirect: + return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -304,9 +311,14 @@ redirect=redirect, message=message, status='info' ) ) - if not redirect: - redirect = url_for( '/' ) - return trans.response.send_redirect( redirect ) + if redirect: + return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + redirect=redirect, + message=message, + status='info' ) ) else: message = error status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Use javascript:void(0) rather than # in tool section links to avoid unwanted scrolling to top of page.
by Bitbucket 12 Apr '12

12 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a30f98b4b463/ changeset: a30f98b4b463 user: jgoecks date: 2012-04-12 21:36:06 summary: Use javascript:void(0) rather than # in tool section links to avoid unwanted scrolling to top of page. affected #: 2 files diff -r de28eda68d0c40f1a71c5ebf95e06cb816dc890b -r a30f98b4b463f32a133f7a42d36411f0f9e63658 static/scripts/handlebars/compiled/panel_section.js --- a/static/scripts/handlebars/compiled/panel_section.js +++ b/static/scripts/handlebars/compiled/panel_section.js @@ -10,7 +10,7 @@ stack1 = foundHelper || depth0.id; if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } - buffer += escapeExpression(stack1) + "\">\n <a href=\"#\"><span>"; + buffer += escapeExpression(stack1) + "\">\n <a href=\"javascript:void(0)\"><span>"; foundHelper = helpers.name; stack1 = foundHelper || depth0.name; if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } diff -r de28eda68d0c40f1a71c5ebf95e06cb816dc890b -r a30f98b4b463f32a133f7a42d36411f0f9e63658 static/scripts/handlebars/panel_section.handlebars --- a/static/scripts/handlebars/panel_section.handlebars +++ b/static/scripts/handlebars/panel_section.handlebars @@ -1,5 +1,5 @@ <div class="toolSectionTitle" id="title_{{id}}"> - <a href="#"><span>{{name}}</span></a> + <a href="javascript:void(0)"><span>{{name}}</span></a></div><div id="{{id}}" class="toolSectionBody" style="display: none; "><div class="toolSectionBg"></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix two more places where filenames in content-dispositions were not being surrounded by quotes.
by Bitbucket 12 Apr '12

12 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de28eda68d0c/ changeset: de28eda68d0c user: dan date: 2012-04-12 20:14:45 summary: Fix two more places where filenames in content-dispositions were not being surrounded by quotes. affected #: 2 files diff -r 84d49e39069d965a45097ade1b71a57cdc0a0386 -r de28eda68d0c40f1a71c5ebf95e06cb816dc890b lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -250,7 +250,7 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = data.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) + trans.response.headers["Content-Disposition"] = 'attachment; filename="GalaxyHistoryItem-%s-[%s]%s"' % (data.hid, fname, toext) trans.log_event( "Display dataset id: %s" % str(id) ) try: return open( data.file_name ) diff -r 84d49e39069d965a45097ade1b71a57cdc0a0386 -r de28eda68d0c40f1a71c5ebf95e06cb816dc890b lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1109,7 +1109,7 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' sname = stored.name sname = ''.join(c in valid_chars and c or '_' for c in sname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname ) + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy-Workflow-%s.ga"' % ( sname ) trans.response.set_content_type( 'application/galaxy-archive' ) return stored_dict @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Minor fix for clicking an OpenID provider to refresh credentials.
by Bitbucket 12 Apr '12

12 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/84d49e39069d/ changeset: 84d49e39069d user: dan date: 2012-04-12 18:16:24 summary: Minor fix for clicking an OpenID provider to refresh credentials. affected #: 1 file diff -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 -r 84d49e39069d965a45097ade1b71a57cdc0a0386 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -29,7 +29,7 @@ default_filter = { "openid" : "All" } default_sort_key = "-create_time" columns = [ - grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( operation='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), + grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), grids.GridColumn( "Created", key="create_time", format=time_ago ), ] operations = [ @@ -395,8 +395,6 @@ action='openid_disassociate', use_panels=use_panels, id=kwd['id'] ) ) - elif operation == 'openid_auth': - return trans.response.send_redirect( url_for( controller='user', action='openid_auth', **kwd ) ) kwd['redirect'] = kwd.get( 'redirect', url_for( controller='user', action='openid_manage', use_panels=True ) ) kwd['openid_providers'] = trans.app.openid_providers Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Rework OpenID process.
by Bitbucket 12 Apr '12

12 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d88a9fa7041c/ changeset: d88a9fa7041c user: dan date: 2012-04-12 17:32:01 summary: Rework OpenID process. Add a never_associate_with_user flag to OpenID providers that will prevent an OpenID Provider from being able to be used for logging in to Galaxy. Post authentication actions will still be performed. This is now used for the GenomeSpace OpenID Provider until it is working correctly. affected #: 10 files diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -76,6 +76,7 @@ Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "openid", TEXT, index=True, unique=True ), + Column( "provider", TrimmedString( 255 ) ), ) History.table = Table( "history", metadata, diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 lib/galaxy/model/migrate/versions/0096_openid_provider.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0096_openid_provider.py @@ -0,0 +1,45 @@ +""" +Migration script to add column to openid table for provider. +Remove any OpenID entries with nonunique GenomeSpace Identifier +""" + +BAD_IDENTIFIER = 'https://identity.genomespace.org/identityServer/xrd.jsp' +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import TrimmedString + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + + try: + OpenID_table = Table( "galaxy_user_openid", metadata, autoload=True ) + c = Column( "provider", TrimmedString( 255 ) ) + c.create( OpenID_table ) + assert c is OpenID_table.c.provider + except Exception, e: + print "Adding provider column to galaxy_user_openid table failed: %s" % str( e ) + log.debug( "Adding provider column to galaxy_user_openid table failed: %s" % str( e ) ) + + try: + cmd = "DELETE FROM galaxy_user_openid WHERE openid='%s'" % ( BAD_IDENTIFIER ) + db_session.execute( cmd ) + except Exception, e: + log.debug( "Deleting bad Identifiers from galaxy_user_openid failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + OpenID_table = Table( "galaxy_user_openid", metadata, autoload=True ) + OpenID_table.c.provider.drop() + except Exception, e: + print "Dropping provider column from galaxy_user_openid table failed: %s" % str( e ) + log.debug( "Dropping provider column from galaxy_user_openid table failed: %s" % str( e ) ) \ No newline at end of file diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 lib/galaxy/openid/providers.py --- a/lib/galaxy/openid/providers.py +++ b/lib/galaxy/openid/providers.py @@ -9,6 +9,9 @@ log = logging.getLogger( __name__ ) +NO_PROVIDER_ID = 'None' +RESERVED_PROVIDER_IDS = [ NO_PROVIDER_ID ] + class OpenIDProvider( object ): '''An OpenID Provider object.''' @classmethod @@ -22,7 +25,9 @@ op_endpoint_url = provider_elem.find( 'op_endpoint_url' ) if op_endpoint_url is not None: op_endpoint_url = op_endpoint_url.text + never_associate_with_user = string_as_bool( provider_elem.get( 'never_associate_with_user', 'False' ) ) assert (provider_id and provider_name and op_endpoint_url), Exception( "OpenID Provider improperly configured" ) + assert provider_id not in RESERVED_PROVIDER_IDS, Exception( 'Specified OpenID Provider uses a reserved id: %s' % ( provider_id ) ) sreg_required = [] sreg_optional = [] use_for = {} @@ -45,8 +50,8 @@ sreg_required = None sreg_optional = None use_for = None - return cls( provider_id, provider_name, op_endpoint_url, sreg_required, sreg_optional, use_for, store_user_preference ) - def __init__( self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=None, use_for=None, store_user_preference=None ): + return cls( provider_id, provider_name, op_endpoint_url, sreg_required=sreg_required, sreg_optional=sreg_optional, use_for=use_for, store_user_preference=store_user_preference, never_associate_with_user=never_associate_with_user ) + def __init__( self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=None, use_for=None, store_user_preference=None, never_associate_with_user=None ): '''When sreg options are not specified, defaults are used.''' self.id = id self.name = name @@ -71,6 +76,10 @@ self.store_user_preference = store_user_preference else: self.store_user_preference = {} + if never_associate_with_user: + self.never_associate_with_user = True + else: + self.never_associate_with_user = False def post_authentication( self, trans, openid_manager, info ): sreg_attributes = openid_manager.get_sreg( info ) for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): @@ -80,9 +89,12 @@ raise Exception( 'Only sreg is currently supported.' ) trans.sa_session.add( trans.user ) trans.sa_session.flush() + def has_post_authentication_actions( self ): + return bool( self.store_user_preference ) class OpenIDProviders( object ): '''Collection of OpenID Providers''' + NO_PROVIDER_ID = NO_PROVIDER_ID @classmethod def from_file( cls, filename ): try: @@ -107,6 +119,7 @@ self.providers = providers else: self.providers = odict() + self._banned_identifiers = [ provider.op_endpoint_url for provider in self.providers.itervalues() if provider.never_associate_with_user ] def __iter__( self ): for provider in self.providers.itervalues(): yield provider @@ -115,3 +128,5 @@ return self.providers[ name ] else: return default + def new_provider_from_identifier( self, identifier ): + return OpenIDProvider( None, identifier, identifier, never_associate_with_user = identifier in self._banned_identifiers ) diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -59,7 +59,7 @@ trans.log_event( "Tool id '%s' does not exist" % tool_id ) return "Tool '%s' does not exist, kwd=%s " % (tool_id, kwd) if tool.require_login and not trans.user: - return trans.response.send_redirect( url_for( controller='user', action='login', cntrller='user', message="You must be logged in to use this tool.", status="info", referer=url_for( controller='/tool_runner', action='index', tool_id=tool_id, **kwd ) ) ) + return trans.response.send_redirect( url_for( controller='user', action='login', cntrller='user', message="You must be logged in to use this tool.", status="info", redirect=url_for( controller='/tool_runner', action='index', tool_id=tool_id, **kwd ) ) ) params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers #do param translation here, used by datasource tools if tool.input_translator: diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -11,7 +11,6 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.web.framework.helpers import iff from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password -from galaxy.openid.providers import OpenIDProvider log = logging.getLogger( __name__ ) @@ -30,7 +29,7 @@ default_filter = { "openid" : "All" } default_sort_key = "-create_time" columns = [ - grids.TextColumn( "OpenID URL", key="openid" ), + grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( operation='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), grids.GridColumn( "Created", key="create_time", format=time_ago ), ] operations = [ @@ -48,32 +47,30 @@ return trans.fill_template( '/user/index.mako', cntrller=cntrller, webapp=webapp ) @web.expose def openid_auth( self, trans, webapp='galaxy', **kwd ): + '''Handles user request to access an OpenID provider''' if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) message = 'Unspecified failure authenticating via OpenID' status = kwd.get( 'status', 'done' ) openid_url = kwd.get( 'openid_url', '' ) openid_provider = kwd.get( 'openid_provider', '' ) - referer = kwd.get( 'referer', trans.request.referer ) + if not openid_provider or openid_url: + openid_provider = trans.app.openid_providers.NO_PROVIDER_ID #empty fields cause validation errors + redirect = kwd.get( 'redirect', '' ) auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) action = 'login' - if auto_associate: - action = 'openid_manage' - if not referer: - referer = url_for( '/' ) + if not redirect: + redirect = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) - openid_provider_obj = None - if not openid_url and openid_provider and trans.app.openid_providers.get( openid_provider ): + if openid_url: + openid_provider_obj = trans.app.openid_providers.new_provider_from_identifier( openid_url ) + else: openid_provider_obj = trans.app.openid_providers.get( openid_provider ) - elif openid_url: - openid_provider_obj = OpenIDProvider( openid_url, openid_url, openid_url ) #for manually entered links use the link for id, name and url - elif openid_provider: - message = 'Invalid OpenID provider specified: %s' % ( openid_provider ) - else: + if not openid_url and openid_provider == trans.app.openid_providers.NO_PROVIDER_ID: message = 'An OpenID provider was not specified' - process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate, openid_provider=openid_provider ) - if openid_provider_obj is not None: + elif openid_provider_obj: + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', redirect=redirect, openid_provider=openid_provider, auto_associate=auto_associate ) request = None try: request = consumer.begin( openid_provider_obj.op_endpoint_url ) @@ -87,84 +84,96 @@ redirect_url = request.redirectURL( trans.request.base, process_url ) trans.app.openid_manager.persist_session( trans, consumer ) - trans.response.send_redirect( redirect_url ) - return + return trans.response.send_redirect( redirect_url ) else: form = request.htmlMarkup( trans.request.base, process_url, form_tag_attrs={'id':'openid_message','target':'_top'} ) trans.app.openid_manager.persist_session( trans, consumer ) return form return trans.response.send_redirect( url_for( controller='user', action=action, + redirect=redirect, use_panels=use_panels, message=message, status='error' ) ) @web.expose def openid_process( self, trans, webapp='galaxy', **kwd ): + '''Handle's response from OpenID Providers''' if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) action = 'login' - if auto_associate: + if trans.user: action = 'openid_manage' if trans.app.config.support_url is not None: contact = '<a href="%s">support</a>' % trans.app.config.support_url else: contact = 'support' - message = 'Verification failed for an unknown reason. Please contact support for assistance.' + message = 'Verification failed for an unknown reason. Please contact %s for assistance.' % ( contact ) status = 'error' consumer = trans.app.openid_manager.get_consumer( trans ) info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() - redirect_url = kwd.get( 'referer', url_for( '/' ) ) - openid_provider = kwd.get( 'openid_provider', '' ) + redirect = kwd.get( 'redirect', url_for( '/' ) ) + openid_provider = kwd.get( 'openid_provider', None ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) return trans.response.send_redirect( url_for( controller='user', action=action, use_panels=True, + redirect=redirect, message=message, status='error' ) ) elif info.status == trans.app.openid_manager.SUCCESS: if info.endpoint.canonicalID: display_identifier = info.endpoint.canonicalID + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() - openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + if not openid_provider_obj and user_openid and user_openid.provider: + openid_provider_obj = trans.app.openid_providers.get( user_openid.provider ) if not openid_provider_obj: - openid_provider_obj = OpenIDProvider( display_identifier, display_identifier, display_identifier ) + openid_provider_obj = trans.app.openid_providers.new_provider_from_identifier( display_identifier ) if not user_openid: user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) - elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: + if not user_openid.user: user_openid.session = trans.galaxy_session - elif user_openid.user and not auto_associate: + if not user_openid.provider and openid_provider: + user_openid.provider = openid_provider + if trans.user: + if user_openid.user and user_openid.user.id != trans.user.id: + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + status = "error" + elif not user_openid.user or user_openid.user == trans.user: + if openid_provider_obj.id: + user_openid.provider = openid_provider_obj.id + user_openid.session = trans.galaxy_session + if not openid_provider_obj.never_associate_with_user: + if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "warning" + else: + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "done" + user_openid.user = trans.user + trans.sa_session.add( user_openid ) + trans.sa_session.flush() + trans.log_event( "User associated OpenID: %s" % display_identifier ) + else: + message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) + status ="info" + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) + if redirect: + message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=True, + redirect=redirect, + message=message, + status=status ) ) + elif user_openid.user: trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) - trans.response.send_redirect( redirect_url ) - return - if auto_associate and trans.user: - # The user is already logged in and requested association from - # the user prefs as opposed to using the OpenID form on the - # login page. - if user_openid.user and user_openid.user.id != trans.user.id: - message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) - status = "error" - elif user_openid.user and user_openid.user.id == trans.user.id: - message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) - status = "warning" - else: - user_openid.user_id = trans.user.id - trans.sa_session.add( user_openid ) - trans.sa_session.flush() - trans.log_event( "User associated OpenID: %s" % display_identifier ) - message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) - status = "done" - openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) - trans.response.send_redirect( url_for( controller='user', - action='openid_manage', - use_panels=True, - message=message, - status=status ) ) - return + return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." @@ -179,10 +188,11 @@ email = sreg_resp.get( sreg_email_name, '' ) except AttributeError: email = '' - trans.response.send_redirect( url_for( controller='user', + #OpenID success, but user not logged in, and not previously associated + return trans.response.send_redirect( url_for( controller='user', action='openid_associate', - openid_provider=openid_provider, use_panels=True, + redirect=redirect, username=username, email=email, message=message, @@ -198,10 +208,12 @@ return trans.response.send_redirect( url_for( controller='user', action=action, use_panels=True, + redirect=redirect, message=message, status=status ) ) @web.expose def openid_associate( self, trans, cntrller='user', webapp='galaxy', **kwd ): + '''Associates a user with an OpenID log in''' if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) @@ -209,9 +221,7 @@ status = kwd.get( 'status', 'done' ) email = kwd.get( 'email', '' ) username = kwd.get( 'username', '' ) - referer = kwd.get( 'referer', trans.request.referer ) - openid_provider = kwd.get( 'openid_provider', '' ) - openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + redirect = kwd.get( 'redirect', '' ) params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() openids = trans.galaxy_session.openids @@ -223,18 +233,33 @@ if kwd.get( 'login_button', False ): message, status, user, success = self.__validate_login( trans, webapp, **kwd ) if success: + openid_objs = [] for openid in openids: - openid.user = user - trans.sa_session.add( openid ) + openid_provider_obj = trans.app.openid_providers.get( openid.provider ) + if not openid_provider_obj or not openid_provider_obj.never_associate_with_user: + openid.user = user + trans.sa_session.add( openid ) + trans.log_event( "User associated OpenID: %s" % openid.openid ) + if openid_provider_obj and openid_provider_obj.has_post_authentication_actions(): + openid_objs.append( openid_provider_obj ) trans.sa_session.flush() - for openid in openids: - trans.log_event( "User associated OpenID: %s" % openid.openid ) - redirect_url = referer - if not redirect_url: - redirect_url = url_for( '/' ) - if openid_provider_obj: - return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) - return trans.response.send_redirect( redirect_url ) + if len( openid_objs ) == 1: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_objs[0].id, redirect=redirect, auto_associate=True ) ) + elif openid_objs: + message = 'You have authenticated with several OpenID providers, please click the following links to execute the post authentication actions. ' + message = "%s<br/><ul>" % ( message ) + for openid in openid_objs: + message = '%s<li><a href="%s" target="_blank">%s</a></li>' % ( message, url_for( controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True ), openid.name ) + message = "%s</ul>" % ( message ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=True, + redirect=redirect, + message=message, + status='info' ) ) + if not redirect: + redirect = url_for( '/' ) + return trans.response.send_redirect( redirect ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -253,21 +278,35 @@ subscribe_checked, **kwd ) if success: - trans.handle_user_login( user, webapp ) - trans.log_event( "User created a new account" ) - trans.log_event( "User logged in" ) + openid_objs = [] for openid in openids: - openid.user = user - trans.sa_session.add( openid ) + openid_provider_obj = trans.app.openid_providers.get( openid.provider ) + if not openid_provider_obj: + openid_provider_obj = trans.app.openid_providers.new_provider_from_identifier( openid.identifier ) + if not openid_provider_obj.never_associate_with_user: + openid.user = user + trans.sa_session.add( openid ) + trans.log_event( "User associated OpenID: %s" % openid.openid ) + if openid_provider_obj.has_post_authentication_actions(): + openid_objs.append( openid_provider_obj ) trans.sa_session.flush() - for openid in openids: - trans.log_event( "User associated OpenID: %s" % openid.openid ) - redirect_url = referer - if not redirect_url: - redirect_url = url_for( '/' ) - if openid_provider_obj: - return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) - return trans.response.send_redirect( redirect_url ) + if len( openid_objs ) == 1: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_objs[0].id, redirect=redirect, auto_associate=True ) ) + elif openid_objs: + message = 'You have authenticated with several OpenID providers, please click the following links to execute the post authentication actions. ' + message = "%s<br/><ul>" % ( message ) + for openid in openid_objs: + message = '%s<li><a href="%s" target="_blank">%s</a></li>' % ( message, url_for( controller='user', action='openid_auth', openid_provider=openid.id, redirect=redirect, auto_associate=True ), openid.name ) + message = "%s</ul>" % ( message ) + return trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=True, + redirect=redirect, + message=message, + status='info' ) ) + if not redirect: + redirect = url_for( '/' ) + return trans.response.send_redirect( redirect ) else: message = error status = 'error' @@ -291,8 +330,7 @@ username=username, header='', use_panels=use_panels, - redirect_url='', - referer='', + redirect=redirect, refresh_frames=[], message=message, status=status, @@ -301,11 +339,11 @@ user_type_fd_id_select_field=user_type_fd_id_select_field, user_type_form_definition=user_type_form_definition, widgets=widgets, - openids=openids, - openid_provider=openid_provider ) + openids=openids ) @web.expose @web.require_login( 'manage OpenIDs' ) def openid_disassociate( self, trans, webapp='galaxy', **kwd ): + '''Disassociates a user with an OpenID''' if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) params = util.Params( kwd ) @@ -338,7 +376,7 @@ trans.log_event( "User disassociated OpenID: %s" % deleted_url ) message = '%s OpenIDs were disassociated from your Galaxy account.' % len( ids ) status = 'done' - trans.response.send_redirect( url_for( controller='user', + return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=use_panels, message=message, @@ -346,29 +384,33 @@ @web.expose @web.require_login( 'manage OpenIDs' ) def openid_manage( self, trans, webapp='galaxy', **kwd ): + '''Manage OpenIDs for user''' if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) use_panels = kwd.get( 'use_panels', False ) if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "delete": - trans.response.send_redirect( url_for( controller='user', + return trans.response.send_redirect( url_for( controller='user', action='openid_disassociate', use_panels=use_panels, id=kwd['id'] ) ) - kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) + elif operation == 'openid_auth': + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', **kwd ) ) + + kwd['redirect'] = kwd.get( 'redirect', url_for( controller='user', action='openid_manage', use_panels=True ) ) kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): - referer = kwd.get( 'referer', trans.request.referer ) + '''Handle Galaxy Log in''' + redirect = kwd.get( 'redirect', trans.request.referer ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) header = '' user = None email = kwd.get( 'email', '' ) - openid_provider = kwd.get( 'openid_provider', '' ) if kwd.get( 'login_button', False ): if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: @@ -376,8 +418,8 @@ else: refresh_frames = [ 'masthead', 'history' ] message, status, user, success = self.__validate_login( trans, webapp, **kwd ) - if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ): - redirect_url = referer + if success and redirect and not redirect.startswith( trans.request.base + url_for( controller='user', action='logout' ) ): + redirect_url = redirect elif success: redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: @@ -399,7 +441,7 @@ header=header, use_panels=use_panels, redirect_url=redirect_url, - referer=referer, + redirect=redirect, refresh_frames=refresh_frames, message=message, status=status, @@ -410,7 +452,7 @@ status = kwd.get( 'status', 'done' ) email = kwd.get( 'email', '' ) password = kwd.get( 'password', '' ) - referer = kwd.get( 'referer', trans.request.referer ) + redirect = kwd.get( 'redirect', trans.request.referer ) success = False user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() if not user: @@ -430,7 +472,7 @@ if webapp == 'galaxy': trans.log_event( "User logged in" ) message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( user.email, referer, url_for( '/' ) ) + ( user.email, redirect, url_for( '/' ) ) if trans.app.config.require_login: message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) success = True @@ -470,7 +512,7 @@ username = util.restore_text( params.get( 'username', '' ) ) subscribe = params.get( 'subscribe', '' ) subscribe_checked = CheckboxField.is_checked( subscribe ) - referer = kwd.get( 'referer', trans.request.referer ) + redirect = kwd.get( 'redirect', trans.request.referer ) is_admin = cntrller == 'admin' and trans.user_is_admin if not trans.app.config.allow_user_creation and not trans.user_is_admin(): message = 'User registration is disabled. Please contact your Galaxy administrator for an account.' @@ -534,7 +576,7 @@ widgets=widgets, webapp=webapp, use_panels=use_panels, - referer=referer, + redirect=redirect, redirect_url=redirect_url, refresh_frames=refresh_frames, message=message, diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 openid/genomespace.xml --- a/openid/genomespace.xml +++ b/openid/genomespace.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<provider id="genomespace" name="GenomeSpace"> +<provider id="genomespace" name="GenomeSpace" never_associate_with_user="True"><op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url><sreg><field name="nickname" required="True"> diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -50,7 +50,7 @@ %if trans.app.config.enable_openid: <br/> - ${render_openid_form( referer, False, openid_providers )} + ${render_openid_form( redirect, False, openid_providers )} %endif %endif @@ -59,7 +59,7 @@ </%def> -<%def name="render_login_form( form_action=None, openid_provider='' )"> +<%def name="render_login_form( form_action=None )"><% if form_action is None: @@ -76,8 +76,7 @@ <label>Email address:</label><input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="referer" value="${referer}" size="40"/> - <input type="hidden" name="openid_provider" value="${openid_provider}" /> + <input type="hidden" name="redirect" value="${redirect}" size="40"/></div><div class="form-row"><label>Password:</label> @@ -94,7 +93,7 @@ </%def> -<%def name="render_openid_form( referer, auto_associate, openid_providers )"> +<%def name="render_openid_form( redirect, auto_associate, openid_providers )"><div class="toolForm"><div class="toolFormTitle">OpenID Login</div><form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" target="_parent" > @@ -102,8 +101,7 @@ <label>OpenID URL:</label><input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/><input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="referer" value="${referer}" size="40"/> - <input type="hidden" name="auto_associate" value="${auto_associate}" size="40"/> + <input type="hidden" name="redirect" value="${redirect}" size="40"/></div><div class="form-row"> Or, authenticate with your <select name="openid_provider"> diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -65,11 +65,11 @@ <% form_action = h.url_for( cntrller=cntrller, use_panels=use_panels ) %> - ${render_login_form( form_action=form_action, openid_provider=openid_provider )} + ${render_login_form( form_action=form_action )} <br/> - ${render_registration_form( form_action=form_action, openid_provider=openid_provider )} + ${render_registration_form( form_action=form_action )} </div></div> diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 templates/user/openid_manage.mako --- a/templates/user/openid_manage.mako +++ b/templates/user/openid_manage.mako @@ -7,7 +7,7 @@ <%def name="grid_body( grid )"> ${make_grid( grid )} <h2>Associate more OpenIDs</h2> - ${render_openid_form( kwargs['referer'], True, kwargs['openid_providers'] )} + ${render_openid_form( kwargs['redirect'], True, kwargs['openid_providers'] )} </%def><%def name="center_panel()"> diff -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf -r d88a9fa7041c02f8c448eecb2a86c93b5c47d6a0 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -21,7 +21,7 @@ ${render_registration_form()} %endif -<%def name="render_registration_form( form_action=None, openid_provider='' )"> +<%def name="render_registration_form( form_action=None )"><% if form_action is None: @@ -37,8 +37,7 @@ <label>Email address:</label><input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="referer" value="${referer}" size="40"/> - <input type="hidden" name="openid_provider" value="${openid_provider}" /> + <input type="hidden" name="redirect" value="${redirect}" size="40"/></div><div class="form-row"><label>Password:</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Remove enable_api flag; API is now enabled by default and cannot be disabled.
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8376ad08ae41/ changeset: 8376ad08ae41 user: jgoecks date: 2012-04-11 20:45:44 summary: Remove enable_api flag; API is now enabled by default and cannot be disabled. affected #: 9 files diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -42,8 +42,6 @@ tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) - # web API - self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -103,37 +103,37 @@ webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) - # If enabled, add the web API - if asbool( kwargs.get( 'enable_api', False ) ): - add_api_controllers( webapp, app ) - webapp.api_mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) - webapp.api_mapper.resource( 'content', - 'contents', - controller='history_contents', - name_prefix='history_', - path_prefix='/api/histories/:history_id', - parent_resources=dict( member_name='history', collection_name='histories' ) ) - webapp.api_mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) - webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) - webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) - webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) - webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) - webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) - webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) - webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) - webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) - #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) + + # Add the web API + add_api_controllers( webapp, app ) + webapp.api_mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'content', + 'contents', + controller='history_contents', + name_prefix='history_', + path_prefix='/api/histories/:history_id', + parent_resources=dict( member_name='history', collection_name='histories' ) ) + webapp.api_mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) + webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) + webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) + webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) + webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) + webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) + webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) + webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -625,9 +625,6 @@ or not scp_configs.get( 'user_name', '' ) \ or not scp_configs.get( 'password', '' ): err_msg += "Error in external service login information. " - # Make sure web API is enabled and API key exists - if not trans.app.config.enable_api: - err_msg += "The 'enable_api = True' setting is not correctly set in the Galaxy config file. " if not trans.user.api_keys: err_msg += "Set your API Key in your User Preferences to transfer datasets. " # Check if library_import_dir is set diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -39,8 +39,6 @@ self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) - # web API - self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf scripts/api/README --- a/scripts/api/README +++ b/scripts/api/README @@ -3,7 +3,6 @@ Set these options in universe_wsgi.ini and start the server: -enable_api = True admin_users = you(a)example.org library_import_dir = /path/to/some/directory diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -12,9 +12,7 @@ %if webapp == 'galaxy': <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, webapp=webapp )}">${_('Manage your information')}</a></li><li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller, webapp=webapp )}">${_('Change default permissions')}</a> for new histories</li> - %if trans.app.config.enable_api: - <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller, webapp=webapp )}">${_('Manage your API keys')}</a></li> - %endif + <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller, webapp=webapp )}">${_('Manage your API keys')}</a></li> %if trans.app.config.enable_openid: <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller, webapp=webapp )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -166,8 +166,7 @@ menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_pages', False ): menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) - if app.config.enable_api: - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.use_remote_user: menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf test/functional/test_sample_tracking.py --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -853,7 +853,7 @@ sample_dataset_ids = [ self.security.encode_id( dataset.id ) for dataset in request1_sample1.datasets ] strings_displayed = [ 'Manage "%s" datasets' % request1_sample1.name ] strings_displayed_count = [ ( galaxy.model.SampleDataset.transfer_status.NOT_STARTED, len( request1_sample1.datasets ) ) ] - strings_displayed_after_submit = [ "Error in sequencer login information. The 'enable_api = True' setting is not correctly set in the Galaxy config file. Set your API Key in your User Preferences to transfer datasets." ] + strings_displayed_after_submit = [ "Error in sequencer login information. Please set your API Key in your User Preferences to transfer datasets." ] strings_not_displayed = [ galaxy.model.SampleDataset.transfer_status.IN_QUEUE, galaxy.model.SampleDataset.transfer_status.TRANSFERRING, galaxy.model.SampleDataset.transfer_status.ADD_TO_LIBRARY, diff -r bb7f51fb545d0517eeceb902fa83dc5a659c64df -r 8376ad08ae41b9b7efa06622b031cb731e2c0bcf universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -504,9 +504,6 @@ #enable_openid = False #openid_config_file = openid_conf.xml -# Enable the (experimental! beta!) Web API. Documentation forthcoming. -#enable_api = False - # Optional list of email addresses of API users who can make calls on behalf of # other users #api_allow_run_as = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Tabular dataset display - Remove logs, revert scroll detection to base.
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb7f51fb545d/ changeset: bb7f51fb545d user: dannon date: 2012-04-11 18:03:51 summary: Tabular dataset display - Remove logs, revert scroll detection to base. affected #: 1 file diff -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d -r bb7f51fb545d0517eeceb902fa83dc5a659c64df templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -39,11 +39,7 @@ $(document).ready(function(){ fillTable(); $(window).scroll(function(){ - console.log($(window).scrollTop()); - console.log($(document).height()); - console.log($(window).height()); - // if ($(window).scrollTop() == $(document).height() - $(window).height()){ - if ($(document).height() - $(window).scrollTop() <= $(window).height()){ + if ($(window).scrollTop() == $(document).height() - $(window).height()){ fillTable(); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Incremental display for tabular datatypes.
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ff62ddc66b1a/ changeset: ff62ddc66b1a user: dannon date: 2012-04-11 17:52:52 summary: Incremental display for tabular datatypes. affected #: 9 files diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -34,6 +34,17 @@ """Returns the mime type of the datatype""" return 'application/octet-stream' + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): + trans.response.set_content_type(dataset.get_mime()) + trans.log_event( "Display dataset id: %s" % str( dataset.id ) ) + trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size ) + to_ext = dataset.extension + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150] + trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext) + return open( dataset.file_name ) + class Ab1( Binary ): """Class describing an ab1 binary sequence file""" file_ext = "ab1" diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -39,7 +39,7 @@ 'test' >>> type( DataTest.metadata_spec.test.param ) <class 'galaxy.datatypes.metadata.MetadataParameter'> - + """ __metaclass__ = DataMeta # Add metadata elements @@ -60,7 +60,7 @@ primary_file_name = 'index' #A per datatype setting (inherited): max file size (in bytes) for setting optional metadata _max_optional_metadata_filesize = None - + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) @@ -118,7 +118,7 @@ to_check = dataset.metadata.items() for key, value in to_check: if key in skip or ( not check and dataset.metadata.spec[key].get( "optional" ) ): - continue #we skip check for optional and nonrequested values here + continue #we skip check for optional and nonrequested values here if not value: return True return False @@ -142,6 +142,7 @@ else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + def display_peek(self, dataset ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] @@ -163,6 +164,158 @@ except Exception, exc: out = "Can't create peek %s" % str( exc ) return out + + def _archive_composite_dataset( self, trans, data=None, **kwd ): + # save a composite object into a compressed archive for downloading + params = util.Params( kwd ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + outfname = data.name[0:150] + outfname = ''.join(c in valid_chars and c or '_' for c in outfname) + if (params.do_action == None): + params.do_action = 'zip' # default + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if not data: + msg = "You must select at least one dataset" + messagetype = 'error' + else: + error = False + try: + if (params.do_action == 'zip'): + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + if ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif params.do_action == 'tgz': + archive = util.streamball.StreamBall( 'w|gz' ) + elif params.do_action == 'tbz': + archive = util.streamball.StreamBall( 'w|bz2' ) + except (OSError, zipfile.BadZipFile): + error = True + log.exception( "Unable to create archive for download" ) + msg = "Unable to create archive for %s for download, please report this error" % outfname + messagetype = 'error' + if not error: + current_user_roles = trans.get_current_user_roles() + ext = data.extension + path = data.file_name + fname = os.path.split(path)[-1] + efp = data.extra_files_path + htmlname = os.path.splitext(outfname)[0] + if not htmlname.endswith(ext): + htmlname = '%s_%s' % (htmlname,ext) + archname = '%s.html' % htmlname # fake the real nature of the html file + try: + archive.add(data.file_name,archname) + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue + if not error: + if params.do_action == 'zip': + archive.close() + tmpfh = open( tmpf ) + # CANNOT clean up - unlink/rmdir was always failing because file handle retained to return - must rely on a cron job to clean up tmp + trans.response.set_content_type( "application/x-zip-compressed" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.zip"' % outfname + return tmpfh + else: + trans.response.set_content_type( "application/x-tar" ) + outext = 'tgz' + if params.do_action == 'tbz': + outext = 'tbz' + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (outfname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + return trans.show_error_message( msg ) + + def _serve_raw(self, trans, dataset, to_ext): + trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150] + trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext) + return open( dataset.file_name ) + + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): + """ Old display method, for transition """ + #Relocate all composite datatype display to a common location. + composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) + composite_extensions.append('html') # for archiving composite datatypes + if isinstance( dataset, basestring ): + return dataset + if filename and filename != "index": + # For files in extra_files_path + file_path = trans.app.object_store.get_filename(dataset, extra_dir='dataset_%s_files' % dataset.id, alt_name=filename) + if os.path.exists( file_path ): + if os.path.isdir( file_path ): + return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories? + mime, encoding = mimetypes.guess_type( file_path ) + if not mime: + try: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) + except: + mime = "text/plain" + trans.response.set_content_type( mime ) + return open( file_path ) + else: + return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) + trans.response.set_content_type(dataset.get_mime()) + trans.log_event( "Display dataset id: %s" % str( dataset.id ) ) + from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR + if to_ext or isinstance(dataset.datatype, datatypes.binary.Binary): # Saving the file, or binary file + if dataset.extension in composite_extensions: + return self._archive_composite_dataset( trans, dataset, **kwd ) + else: + trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size ) + if not to_ext: + to_ext = dataset.extension + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150] + trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext) + return open( dataset.file_name ) + if not os.path.exists( dataset.file_name ): + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % dataset.file_name ) + max_peek_size = 1000000 # 1 MB + if isinstance(dataset.datatype, datatypes.images.Html): + max_peek_size = 10000000 # 10 MB for html + if not preview or isinstance(dataset.datatype, datatypes.images.Image) or os.stat( dataset.file_name ).st_size < max_peek_size: + if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html": + # Sanitize anytime we respond with plain text/html content. + return sanitize_html(open( dataset.file_name ).read()) + return open( dataset.file_name ) + else: + trans.response.set_content_type( "text/html" ) + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( dataset.file_name ).read(max_peek_size), + data = dataset ) + """Returns dataset contents for display. + This allows for customization of subtype displays""" + file_path = trans.app.object_store.get_filename(dataset, extra_dir='dataset_%s_files' % dataset.id, alt_name=filename) + if size: + return open(dataset.file_path).read(size) + else: + open(dataset.file_path) + def display_name(self, dataset): """Returns formatted html of dataset name""" try: @@ -183,11 +336,11 @@ info = info.replace( '\r', '<br/>' ) if info.find( '\n' ) >= 0: info = info.replace( '\n', '<br/>' ) - + # Convert to unicode to display non-ascii characters. if type( info ) is not unicode: info = unicode( info, 'utf-8') - + return info except: return "info unavailable" @@ -272,7 +425,7 @@ def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, set_output_history=True): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type ) - + if converter is None: raise Exception( "A converter does not exist for %s to %s." % ( original_dataset.ext, target_type ) ) #Generate parameter dictionary @@ -284,7 +437,7 @@ params[value.name] = deps[value.name] elif value.type == 'data': input_name = key - + params[input_name] = original_dataset #Run converter, job is dispatched through Queue converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] @@ -351,18 +504,18 @@ @property def has_resolution(self): return False - - - def merge( split_files, output_file): + + + def merge( split_files, output_file): """ TODO: Do we need to merge gzip files using gzjoin? cat seems to work, but might be brittle. Need to revisit this. """ if len(split_files) == 1: - cmd = 'mv -f %s %s' % ( split_files[0], output_file ) + cmd = 'mv -f %s %s' % ( split_files[0], output_file ) else: - cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) + cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) result = os.system(cmd) if result != 0: raise Exception('Result %s from %s' % (result, cmd)) @@ -377,7 +530,7 @@ def write_from_stream(self, dataset, stream): """Writes data from a stream""" - # write it twice for now + # write it twice for now fd, temp_name = tempfile.mkstemp() while 1: chunk = stream.read(1048576) @@ -468,11 +621,11 @@ """ if split_params is None: return - + if len(input_datasets) > 1: raise Exception("Text file splitting does not support multiple files") input_files = [ds.file_name for ds in input_datasets] - + lines_per_file = None chunk_size = None if split_params['split_mode'] == 'number_of_parts': @@ -501,7 +654,7 @@ chunk_size = int(split_params['split_size']) else: raise Exception('Unsupported split mode %s' % split_params['split_mode']) - + f = open(input_files[0], 'rt') try: chunk_idx = 0 @@ -562,7 +715,7 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ): """ Returns the first LINE_COUNT lines wrapped to WIDTH - + ## >>> fname = get_test_fname('4.bed') ## >>> get_file_peek(fname) ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' @@ -601,11 +754,12 @@ lines.append( line ) count += 1 temp.close() - if file_type in [ 'gzipped', 'binary' ]: - text = "%s file" % file_type + if file_type in [ 'gzipped', 'binary' ]: + text = "%s file" % file_type else: try: text = unicode( '\n'.join( lines ), 'utf-8' ) except UnicodeDecodeError: text = "binary/unknown file" return text + diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -13,11 +13,13 @@ from galaxy.datatypes.metadata import MetadataElement import galaxy_utils.sequence.vcf from sniff import * +from galaxy.util.json import to_json_string log = logging.getLogger(__name__) class Tabular( data.Text ): """Tab delimited data""" + CHUNK_SIZE = 20000 """Add metadata elements""" MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) @@ -33,15 +35,15 @@ that contain numerical values in the dataset. A skip parameter is used because various tabular data types reuse this function, and their data type classes are responsible to determine how many invalid - comment lines should be skipped. Using None for skip will cause skip - to be zero, but the first line will be processed as a header. A - max_data_lines parameter is used because various tabular data types - reuse this function, and their data type classes are responsible to + comment lines should be skipped. Using None for skip will cause skip + to be zero, but the first line will be processed as a header. A + max_data_lines parameter is used because various tabular data types + reuse this function, and their data type classes are responsible to determine how many data lines should be processed to ensure that the - non-optional metadata parameters are properly set; if used, optional - metadata parameters will be set to None, unless the entire file has - already been read. Using None (default) for max_data_lines will - process all data lines. + non-optional metadata parameters are properly set; if used, optional + metadata parameters will be set to None, unless the entire file has + already been read. Using None (default) for max_data_lines will + process all data lines. Items of interest: 1. We treat 'overwrite' as always True (we always want to set tabular metadata when called). @@ -58,7 +60,7 @@ column_type_set_order = [ 'int', 'float', 'list', 'str' ] #Order to set column types in default_column_type = column_type_set_order[-1] # Default column type is lowest in list column_type_compare_order = list( column_type_set_order ) #Order to compare column types - column_type_compare_order.reverse() + column_type_compare_order.reverse() def type_overrules_type( column_type1, column_type2 ): if column_type1 is None or column_type1 == column_type2: return False @@ -75,13 +77,13 @@ try: int( column_text ) return True - except: + except: return False def is_float( column_text ): try: float( column_text ) return True - except: + except: if column_text.strip().lower() == 'na': return True #na is special cased to be a float return False @@ -126,7 +128,7 @@ if type_overrules_type( column_type, column_types[field_count] ): column_types[field_count] = column_type if i == 0 and requested_skip is None: - # This is our first line, people seem to like to upload files that have a header line, but do not + # This is our first line, people seem to like to upload files that have a header line, but do not # start with '#' (i.e. all column types would then most likely be detected as str). We will assume # that the first line is always a header (this was previous behavior - it was always skipped). When # the requested skip is None, we only use the data from the first line if we have no other data for @@ -148,7 +150,7 @@ break i += 1 dataset_fh.close() - + #we error on the larger number of columns #first we pad our column_types by using data from first line if len( first_line_column_types ) > len( column_types ): @@ -177,6 +179,7 @@ except Exception, exc: out = "Can't create peek %s" % str( exc ) return out + def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ): out = [] try: @@ -212,6 +215,7 @@ except Exception, exc: raise Exception, "Can't create peek header %s" % str( exc ) return "".join( out ) + def make_html_peek_rows( self, dataset, skipchars=[], **kwargs ): out = [] try: @@ -233,6 +237,28 @@ except Exception, exc: raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out ) + + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): + #TODO Prevent failure when displaying extremely long > 50kb lines. + if to_ext: + return self._serve_raw(trans, dataset, to_ext) + if chunk: + ck_index = int(chunk) + f = open(dataset.file_name) + f.seek(ck_index * self.CHUNK_SIZE) + # If we aren't at the start of the file, seek to next newline. Do this better eventually. + if f.tell() != 0: + cursor = f.read(1) + while cursor and cursor != '\n': + cursor = f.read(1) + ck_data = f.read(self.CHUNK_SIZE) + cursor = f.read(1) + while cursor and ck_data[-1] != '\n': + ck_data += cursor + cursor = f.read(1) + return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) + return trans.fill_template( "/dataset/tabular_chunked.mako",dataset = dataset) + def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) if dataset.metadata.comment_lines: @@ -281,7 +307,7 @@ def sniff( self, filename ): """ Determines whether the file is in SAM format - + A file in SAM format consists of lines of tab-separated data. The following header line may be the first line: @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL @@ -290,12 +316,12 @@ Data in the OPT column is optional and can consist of tab-separated data For complete details see http://samtools.sourceforge.net/SAM1.pdf - + Rules for sniffing as True: There must be 11 or more columns of data on each line Columns 2 (FLAG), 4(POS), 5 (MAPQ), 8 (MPOS), and 9 (ISIZE) must be numbers (9 can be negative) We will only check that up to the first 5 alignments are correctly formatted. - + >>> fname = get_test_fname( 'sequence.maf' ) >>> Sam().sniff( fname ) False @@ -311,7 +337,7 @@ line = line.strip() if not line: break #EOF - if line: + if line: if line[0] != '@': linePieces = line.split('\t') if len(linePieces) < 11: @@ -373,10 +399,10 @@ if result != 0: raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) - + def get_track_type( self ): return "ReadTrack", {"data": "bam", "index": "summary_tree"} - + class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" @@ -402,7 +428,7 @@ """ Checks for 'pileup-ness' - There are two main types of pileup: 6-column and 10-column. For both, + There are two main types of pileup: 6-column and 10-column. For both, the first three and last two columns are the same. We only check the first three to allow for some personalization of the format. @@ -436,27 +462,27 @@ class ElandMulti( Tabular ): file_ext = 'elandmulti' - + def sniff( self, filename ): return False - + class Vcf( Tabular ): """ Variant Call Format for describing SNPs and other simple genome variations. """ - + file_ext = 'vcf' column_names = [ 'Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data' ] - + MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True ) - + def sniff( self, filename ): headers = get_headers( filename, '\n', count=1 ) return headers[0][0].startswith("##fileformat=VCF") def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names ) - + def get_track_type( self ): return "VcfTrack", {"data": "tabix", "index": "summary_tree"} @@ -500,10 +526,10 @@ def sniff( self, filename ): """ Determines whether the file is in ELAND export format - + A file in ELAND export format consists of lines of tab-separated data. There is no header. - + Rules for sniffing as True: There must be 22 columns on each line LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct @@ -522,7 +548,7 @@ line = line.strip() if not line: break #EOF - if line: + if line: linePieces = line.split('\t') if len(linePieces) != 22: return False @@ -568,7 +594,7 @@ #else: # # Otherwise, read the whole thing and set num data lines. for i, line in enumerate(dataset_fh): - if line: + if line: linePieces = line.split('\t') if len(linePieces) != 22: raise Exception('%s:%d:Corrupt line!' % (dataset.file_name,i)) @@ -586,5 +612,5 @@ dataset.metadata.tiles = ["%04d" % int(t) for t in tiles.keys()] dataset.metadata.barcodes = filter(lambda x: x != '0', barcodes.keys()) + ['NoIndex' for x in barcodes.keys() if x == '0'] dataset.metadata.reads = reads.keys() - - + + diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -1,17 +1,22 @@ -import logging, os, string, shutil, re, socket, mimetypes, urllib, tempfile, zipfile, glob, sys +import logging +import mimetypes +import os +import string +import sys +import tempfile +import urllib +import zipfile from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy import util, datatypes, jobs, web, model -from cgi import escape, FieldStorage +from galaxy import util, datatypes, web, model from galaxy.datatypes.display_applications.util import encode_dataset_user, decode_dataset_user from galaxy.util.sanitize_html import sanitize_html from galaxy.util import inflector from galaxy.model.item_attrs import * -from galaxy.model import LibraryDatasetDatasetAssociation, HistoryDatasetAssociation from galaxy.web.framework.helpers import to_unicode -import pkg_resources; +import pkg_resources; pkg_resources.require( "Paste" ) import paste.httpexceptions @@ -32,7 +37,7 @@ except RuntimeError: log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) except (TypeError, zipfile.LargeZipFile): # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped - log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) + log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) comptypes.append( 'zip' ) try: os.unlink( tmpf ) @@ -53,7 +58,7 @@ ----------------------------------------------------------------------------- You should be able to view the history containing the related history item -${hid}: ${history_item_name} +${hid}: ${history_item_name} by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. @@ -90,7 +95,7 @@ class HistoryColumn( grids.GridColumn ): def get_value( self, trans, grid, hda): return hda.history.name - + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -111,19 +116,19 @@ template='/dataset/grid.mako' default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", + grids.TextColumn( "Name", key="name", # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), - HistoryColumn( "History", key="history", + HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] - columns.append( - grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[2] ], + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ @@ -136,17 +141,17 @@ num_rows_per_page = 50 def build_initial_query( self, trans, **kwargs ): # Show user's datasets that are not deleted, not in deleted histories, and not hidden. - # To filter HDAs by user, need to join model class/HDA and History table so that it is - # possible to filter by user. However, for dictionary-based filtering to work, need a + # To filter HDAs by user, need to join model class/HDA and History table so that it is + # possible to filter by user. However, for dictionary-based filtering to work, need a # primary table for the query. return trans.sa_session.query( self.model_class ).select_from( self.model_class.table.join( model.History.table ) ) \ .filter( model.History.user == trans.user ) \ .filter( self.model_class.deleted==False ) \ .filter( model.History.deleted==False ) \ .filter( self.model_class.visible==True ) - + class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHistoryDatasetAssociation, UsesItemRatings ): - + stored_list_grid = HistoryDatasetAssociationListGrid() @web.expose @@ -202,7 +207,7 @@ job_stdout=job.stdout, job_info=job.info, job_traceback=job.traceback, - email=email, + email=email, message=message ) frm = to_address # Check email a bit @@ -219,130 +224,45 @@ return trans.show_ok_message( "Your error report has been sent" ) except Exception, e: return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) - + @web.expose def default(self, trans, dataset_id=None, **kwd): return 'This link may not be followed from within Galaxy.' - - @web.expose - def archive_composite_dataset( self, trans, data=None, **kwd ): - # save a composite object into a compressed archive for downloading - params = util.Params( kwd ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - outfname = data.name[0:150] - outfname = ''.join(c in valid_chars and c or '_' for c in outfname) - if (params.do_action == None): - params.do_action = 'zip' # default - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if not data: - msg = "You must select at least one dataset" - messagetype = 'error' - else: - error = False - try: - if (params.do_action == 'zip'): - # Can't use mkstemp - the file must not exist first - tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) - if ziptype == '64': - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) - else: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) - archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) - elif params.do_action == 'tgz': - archive = util.streamball.StreamBall( 'w|gz' ) - elif params.do_action == 'tbz': - archive = util.streamball.StreamBall( 'w|bz2' ) - except (OSError, zipfile.BadZipFile): - error = True - log.exception( "Unable to create archive for download" ) - msg = "Unable to create archive for %s for download, please report this error" % outfname - messagetype = 'error' - if not error: - current_user_roles = trans.get_current_user_roles() - ext = data.extension - path = data.file_name - fname = os.path.split(path)[-1] - efp = data.extra_files_path - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname,ext) - archname = '%s.html' % htmlname # fake the real nature of the html file - try: - archive.add(data.file_name,archname) - except IOError: - error = True - log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - for root, dirs, files in os.walk(efp): - for fname in files: - fpath = os.path.join(root,fname) - rpath = os.path.relpath(fpath,efp) - try: - archive.add( fpath,rpath ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % rpath) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue - if not error: - if params.do_action == 'zip': - archive.close() - tmpfh = open( tmpf ) - # CANNOT clean up - unlink/rmdir was always failing because file handle retained to return - must rely on a cron job to clean up tmp - trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.zip"' % outfname - return tmpfh - else: - trans.response.set_content_type( "application/x-tar" ) - outext = 'tgz' - if params.do_action == 'tbz': - outext = 'tbz' - trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (outfname,outext) - archive.wsgi_status = trans.response.wsgi_status() - archive.wsgi_headeritems = trans.response.wsgi_headeritems() - return archive.stream - return trans.show_error_message( msg ) - + @web.expose def get_metadata_file(self, trans, hda_id, metadata_name): """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """ data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) ) if not data or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) - + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] - + file_ext = data.metadata.spec.get(metadata_name).get("file_ext", metadata_name) trans.response.headers["Content-Type"] = "application/octet-stream" trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, fname, file_ext) return open(data.metadata.get(metadata_name).file_name) - - def _check_dataset(self, trans, dataset_id): + + def _check_dataset(self, trans, hda_id): # DEPRECATION: We still support unencoded ids for backward compatibility try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id) ) if data is None: - raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + raise ValueError( 'Invalid reference dataset id: %s.' % hda_id) except: try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( hda_id ) ) except: data = None if not data: - raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) + raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( hda_id ) ) if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) - if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - return data - + @web.expose @web.json def transfer_status(self, trans, dataset_id, filename=None): @@ -352,7 +272,7 @@ if isinstance( data, basestring ): return data log.debug( "Checking transfer status for dataset %s..." % data.dataset.id ) - + # Pulling files in extra_files_path into cache is not handled via this # method but that's primarily because those files are typically linked to # through tool's output page anyhow so tying a JavaScript event that will @@ -361,63 +281,11 @@ return True else: return trans.app.object_store.file_ready(data.dataset) - + @web.expose - def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) - composite_extensions.append('html') # for archiving composite datatypes + def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd): data = self._check_dataset(trans, dataset_id) - if isinstance( data, basestring ): - return data - - if filename and filename != "index": - # For files in extra_files_path - file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) - if os.path.exists( file_path ): - if os.path.isdir( file_path ): - return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories? - mime, encoding = mimetypes.guess_type( file_path ) - if not mime: - try: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) - except: - mime = "text/plain" - trans.response.set_content_type( mime ) - return open( file_path ) - else: - return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - - trans.response.set_content_type(data.get_mime()) - trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - - if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file - if data.extension in composite_extensions: - return self.archive_composite_dataset( trans, data, **kwd ) - else: - trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) - if not to_ext: - to_ext = data.extension - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] - trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename - trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, fname, to_ext) - return open( data.file_name ) - if not os.path.exists( data.file_name ): - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) - max_peek_size = 1000000 # 1 MB - if isinstance(data.datatype, datatypes.images.Html): - max_peek_size = 10000000 # 10 MB for html - if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: - if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html": - # Sanitize anytime we respond with plain text/html content. - return sanitize_html(open( data.file_name ).read()) - return open( data.file_name ) - else: - trans.response.set_content_type( "text/html" ) - return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data = open( data.file_name ).read(max_peek_size), - data = data ) + return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) @web.expose def edit(self, trans, dataset_id=None, filename=None, hid=None, **kwd): @@ -443,7 +311,7 @@ # TODO: hid handling data = history.datasets[ int( hid ) - 1 ] id = None - elif dataset_id is not None: + elif dataset_id is not None: id = trans.app.security.decode_id( dataset_id ) data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) else: @@ -463,7 +331,7 @@ # permission. In this case, we'll reset this permission to the hda user's private role. manage_permissions_action = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action ) permissions = { manage_permissions_action : [ trans.app.security_agent.get_private_user_role( data.history.user ) ] } - trans.app.security_agent.set_dataset_permission( data.dataset, permissions ) + trans.app.security_agent.set_dataset_permission( data.dataset, permissions ) if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." ) @@ -600,7 +468,7 @@ refresh_frames=refresh_frames ) else: return trans.show_error_message( "You do not have permission to edit this dataset's ( id: %s ) information." % str( dataset_id ) ) - + @web.expose @web.require_login( "see all available datasets" ) def list( self, trans, **kwargs ): @@ -610,7 +478,7 @@ if 'operation' in kwargs: operation = kwargs['operation'].lower() hda_ids = util.listify( kwargs.get( 'id', [] ) ) - + # Display no message by default status, message = None, None @@ -630,15 +498,15 @@ if hdas: if operation == "switch" or operation == "switch_history": # Switch to a history that the HDA resides in. - + # Convert hda to histories. histories = [] for hda in hdas: histories.append( hda.history ) - + # Use history controller to switch the history. TODO: is this reasonable? status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) - + # Current history changed, refresh history frame; if switching to a dataset, set hda seek. trans.template_context['refresh_frames'] = ['history'] if operation == "switch": @@ -648,35 +516,35 @@ # Copy a dataset to the current history. target_histories = [ trans.get_history() ] status, message = self._copy_datasets( trans, hda_ids, target_histories ) - + # Current history changed, refresh history frame. trans.template_context['refresh_frames'] = ['history'] # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) - + @web.expose def imp( self, trans, dataset_id=None, **kwd ): """ Import another user's dataset via a shared URL; dataset is added to user's current history. """ msg = "" - + # Set referer message. referer = trans.request.referer if referer is not "": referer_message = "<a href='%s'>return to the previous page</a>" % referer else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) - + # Error checking. if not dataset_id: return trans.show_error_message( "You must specify a dataset to import. You can %s." % referer_message, use_panels=True ) - + # Do import. cur_history = trans.get_history( create=True ) status, message = self._copy_datasets( trans, [ dataset_id ], [ cur_history ], imported=True ) message = "Dataset imported. <br>You can <a href='%s'>start using the dataset</a> or %s." % ( url_for('/'), referer_message ) return trans.show_message( message, type=status, use_panels=True ) - + @web.expose @web.json @web.require_login( "use Galaxy datasets" ) @@ -685,7 +553,7 @@ dataset = self.get_dataset( trans, id, False, True ) return_dict = { "name" : dataset.name, "link" : url_for( action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) ) } return return_dict - + @web.expose def get_embed_html_async( self, trans, id ): """ Returns HTML for embedding a dataset in a page. """ @@ -698,7 +566,7 @@ def set_accessible_async( self, trans, id=None, accessible=False ): """ Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute. """ return - + @web.expose @web.require_login( "rate items" ) @web.json @@ -713,7 +581,7 @@ dataset_rating = self.rate_item( rate_item, trans.get_user(), dataset, rating ) return self.get_ave_item_rating_data( trans.sa_session, dataset ) - + @web.expose def display_by_username_and_slug( self, trans, username, slug, filename=None, preview=True ): """ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """ @@ -722,10 +590,10 @@ # Filename used for composite types. if filename: return self.display( trans, dataset_id=slug, filename=filename) - + truncated, dataset_data = self.get_data( dataset, preview ) dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) - + # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): @@ -741,12 +609,12 @@ else: user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, dataset ) - + return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated, user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) else: raise web.httpexceptions.HTTPNotFound() - + @web.expose def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ @@ -758,7 +626,7 @@ # Get annotation. dataset.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, dataset ) return trans.stream_template_mako( "/dataset/item_content.mako", item=dataset, item_data=dataset_data, truncated=truncated ) - + @web.expose def annotate_async( self, trans, id, new_annotation=None, **kwargs ): dataset = self.get_dataset( trans, id, False, True ) @@ -770,7 +638,7 @@ self.add_item_annotation( trans.sa_session, trans.get_user(), dataset, new_annotation ) trans.sa_session.flush() return new_annotation - + @web.expose def get_annotation_async( self, trans, id ): dataset = self.get_dataset( trans, id, False, True ) @@ -841,7 +709,7 @@ if app_action in [ 'data', 'param' ]: assert action_param, "An action param must be provided for a data or param action" #data is used for things with filenames that could be passed off to a proxy - #in case some display app wants all files to be in the same 'directory', + #in case some display app wants all files to be in the same 'directory', #data can be forced to param, but not the other way (no filename for other direction) #get param name from url param name try: @@ -960,7 +828,7 @@ trans.log_event( "Dataset id %s has been unhidden" % str(id) ) return True return False - + def _purge( self, trans, dataset_id ): message = None status = 'done' @@ -1037,7 +905,7 @@ return "OK" else: raise Exception( message ) - + @web.expose def unhide( self, trans, dataset_id, filename ): if self._unhide( trans, dataset_id ): @@ -1070,7 +938,7 @@ """ Show the parameters used for an HDA """ - + def source_dataset_chain( dataset, lst ): try: cp_from_ldda = dataset.copied_from_library_dataset_dataset_association @@ -1084,13 +952,13 @@ except: pass return lst - + hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) if not hda: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) - + # Get the associated job, if any. If this hda was copied from another, # we need to find the job that created the origial hda params_objects = None @@ -1102,7 +970,7 @@ job = None for assoc in job_hda.creating_job_associations: job = assoc.job - break + break if job: # Get the tool object try: @@ -1113,10 +981,10 @@ params_objects = job.get_param_values( trans.app ) except: pass - + inherit_chain = source_dataset_chain(hda, []) return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, tool=tool, params_objects=params_objects ) - + @web.expose def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): params = util.Params( kwd ) @@ -1175,7 +1043,7 @@ if history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() - hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % + hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % ( url_for( controller="history", action="switch_to_history", \ hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ for hist in target_histories ] ) @@ -1186,7 +1054,7 @@ source_datasets = history.visible_datasets target_histories = [history] if user: - target_histories = user.active_histories + target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", source_history = history, current_history = trans.get_history(), @@ -1204,7 +1072,7 @@ """ Helper method for copying datasets. """ user = trans.get_user() done_msg = error_msg = "" - + invalid_datasets = 0 if not dataset_ids or not target_histories: error_msg = "You must provide both source datasets and target histories." @@ -1229,7 +1097,7 @@ done_msg = "%i dataset%s copied to %i histor%s." % \ ( num_datasets_copied, iff( num_datasets_copied == 1, "", "s"), len( target_histories ), iff( len ( target_histories ) == 1, "y", "ies") ) trans.sa_session.refresh( history ) - + if error_msg != "": status = ERROR message = error_msg diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1700,5 +1700,22 @@ position: relative; } +// Dataset Display Styles + +#loading_indicator{ + position:fixed; + right:10px; + top:10px; + height:32px; + width:32px; + background:url(largespinner.gif); +} + +#content_table td{ + text-align:right; + white-space:nowrap; + padding:2px 10px; +} + @import "base_sprites"; diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -723,6 +723,8 @@ div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} +#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;background:url(largespinner.gif);} +#content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d static/june_2007_style/blue/largespinner.gif Binary file static/june_2007_style/blue/largespinner.gif has changed diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d templates/dataset/tabular_chunked.mako --- /dev/null +++ b/templates/dataset/tabular_chunked.mako @@ -0,0 +1,65 @@ +<%inherit file="/base.mako"/> + + +<%def name="title()">Dataset Display</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; + var DATASET_COLS = ${dataset.metadata.columns}; + var current_chunk = 0; + + function fillTable(){ + if (current_chunk !== -1){ + var table = $('#content_table'); + $.getJSON(DATASET_URL, {chunk: current_chunk}, function (result) { + if (result.ck_data !== ""){ + var lines = result.ck_data.split('\n'); + $.each(lines, function(){ + var line = this; + var cells = line.split('\t'); + /* Check length of cells to ensure this is a complete row. */ + if (cells.length == DATASET_COLS){ + table.append('<tr><td>' + cells.join('</td><td>') + '</td></tr>'); + } + else{ + table.append('<tr><td colspan="'+ DATASET_COLS+ '">' + line + '</td></tr>'); + } + }); + current_chunk = result.ck_index; + } + else { + current_chunk = -1; + } + }); + } + } + + $(document).ready(function(){ + fillTable(); + $(window).scroll(function(){ + console.log($(window).scrollTop()); + console.log($(document).height()); + console.log($(window).height()); + // if ($(window).scrollTop() == $(document).height() - $(window).height()){ + if ($(document).height() - $(window).scrollTop() <= $(window).height()){ + fillTable(); + } + }); + $('#loading_indicator').ajaxStart(function(){ + $(this).show(); + }).ajaxStop(function(){ + $(this).hide(); + }); + }); + </script> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} +</%def> + +<div id="loading_indicator" ></div> +<table id="content_table" cellpadding="0"> +</table> diff -r 60061d1a369635facf858766c7a992272b806750 -r ff62ddc66b1a454e9b3ba11297c0bd8e2a74dc8d templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -361,4 +361,4 @@ </div></div> -</%def> \ No newline at end of file +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Move tools controller from UI controller to an API controller and add show method for tool.
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/60061d1a3696/ changeset: 60061d1a3696 user: jgoecks date: 2012-04-11 17:37:08 summary: Move tools controller from UI controller to an API controller and add show method for tool. affected #: 3 files diff -r 423f4f2910ac90098e799d354a2936513242a21e -r 60061d1a369635facf858766c7a992272b806750 lib/galaxy/web/api/tools.py --- /dev/null +++ b/lib/galaxy/web/api/tools.py @@ -0,0 +1,32 @@ +from galaxy import config, tools, web, util +from galaxy.web.base.controller import BaseController, BaseAPIController + +class ToolsController( BaseAPIController ): + """ + RESTful controller for interactions with tools. + """ + + @web.json + def index( self, trans, **kwds ): + """ + GET /api/tools: returns a list of tools defined by parameters + parameters: + in_panel - if true, tools are returned in panel structure, including sections and labels + trackster - if true, only tools that are compatible with Trackster are returned + """ + + # Read params. + in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) + trackster = util.string_as_bool( kwds.get( 'trackster', 'False' ) ) + + # Create return value. + return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/tools/{tool_id} + Returns tool information, including parameters and inputs. + """ + return self.app.toolbox.tools_by_id[ id ].to_dict( trans, all=True ) + \ No newline at end of file diff -r 423f4f2910ac90098e799d354a2936513242a21e -r 60061d1a369635facf858766c7a992272b806750 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -129,6 +129,7 @@ webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) diff -r 423f4f2910ac90098e799d354a2936513242a21e -r 60061d1a369635facf858766c7a992272b806750 lib/galaxy/web/controllers/tools.py --- a/lib/galaxy/web/controllers/tools.py +++ /dev/null @@ -1,26 +0,0 @@ -from galaxy import config, tools, web, util -from galaxy.web.base.controller import BaseController, BaseUIController - -class ToolsController( BaseUIController ): - """ - RESTful controller for interactions with tools. Once session-based - authentication can be done with API controllers, this will be moved - to be part of the API. - """ - - @web.json - def index( self, trans, **kwds ): - """ - GET /api/tools: returns a list of tools defined by parameters - parameters: - in_panel - if true, tools are returned in panel structure, including sections and labels - trackster - if true, only tools that are compatible with Trackster are returned - """ - - # Read params. - in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) - trackster = util.string_as_bool( kwds.get( 'trackster', 'False' ) ) - - # Create return value. - return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) - \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 11 Apr '12

11 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0a957e499a3c/ changeset: 0a957e499a3c user: jgoecks date: 2012-04-11 16:31:18 summary: Add Backbone-relational library; this is used for managing complex object/collection relationships. affected #: 2 files diff -r bf88ce609370a7829337dad758fafe388b3fd117 -r 0a957e499a3c9b7ba11f88d337e4878260d73d6d static/scripts/libs/backbone-relational.js --- /dev/null +++ b/static/scripts/libs/backbone-relational.js @@ -0,0 +1,1406 @@ +/** + * Backbone-relational.js 0.5.0 + * (c) 2011 Paul Uithol + * + * Backbone-relational may be freely distributed under the MIT license. + * For details and documentation: https://github.com/PaulUithol/Backbone-relational. + * Depends on Backbone: https://github.com/documentcloud/backbone. + */ +( function( undefined ) { + "use strict"; + + /** + * CommonJS shim + **/ + var _, Backbone, exports; + if ( typeof window === 'undefined' ) { + _ = require( 'underscore' ); + Backbone = require( 'backbone' ); + exports = module.exports = Backbone; + } + else { + var _ = window._; + Backbone = window.Backbone; + exports = window; + } + + Backbone.Relational = { + showWarnings: true + }; + + /** + * Semaphore mixin; can be used as both binary and counting. + **/ + Backbone.Semaphore = { + _permitsAvailable: null, + _permitsUsed: 0, + + acquire: function() { + if ( this._permitsAvailable && this._permitsUsed >= this._permitsAvailable ) { + throw new Error( 'Max permits acquired' ); + } + else { + this._permitsUsed++; + } + }, + + release: function() { + if ( this._permitsUsed === 0 ) { + throw new Error( 'All permits released' ); + } + else { + this._permitsUsed--; + } + }, + + isLocked: function() { + return this._permitsUsed > 0; + }, + + setAvailablePermits: function( amount ) { + if ( this._permitsUsed > amount ) { + throw new Error( 'Available permits cannot be less than used permits' ); + } + this._permitsAvailable = amount; + } + }; + + /** + * A BlockingQueue that accumulates items while blocked (via 'block'), + * and processes them when unblocked (via 'unblock'). + * Process can also be called manually (via 'process'). + */ + Backbone.BlockingQueue = function() { + this._queue = []; + }; + _.extend( Backbone.BlockingQueue.prototype, Backbone.Semaphore, { + _queue: null, + + add: function( func ) { + if ( this.isBlocked() ) { + this._queue.push( func ); + } + else { + func(); + } + }, + + process: function() { + while ( this._queue && this._queue.length ) { + this._queue.shift()(); + } + }, + + block: function() { + this.acquire(); + }, + + unblock: function() { + this.release(); + if ( !this.isBlocked() ) { + this.process(); + } + }, + + isBlocked: function() { + return this.isLocked(); + } + }); + /** + * Global event queue. Accumulates external events ('add:<key>', 'remove:<key>' and 'update:<key>') + * until the top-level object is fully initialized (see 'Backbone.RelationalModel'). + */ + Backbone.Relational.eventQueue = new Backbone.BlockingQueue(); + + /** + * Backbone.Store keeps track of all created (and destruction of) Backbone.RelationalModel. + * Handles lookup for relations. + */ + Backbone.Store = function() { + this._collections = []; + this._reverseRelations = []; + }; + _.extend( Backbone.Store.prototype, Backbone.Events, { + _collections: null, + _reverseRelations: null, + + /** + * Add a reverse relation. Is added to the 'relations' property on model's prototype, and to + * existing instances of 'model' in the store as well. + * @param {object} relation + * @param {Backbone.RelationalModel} relation.model + * @param {String} relation.type + * @param {String} relation.key + * @param {String|object} relation.relatedModel + */ + addReverseRelation: function( relation ) { + var exists = _.any( this._reverseRelations, function( rel ) { + return _.all( relation, function( val, key ) { + return val === rel[ key ]; + }); + }); + + if ( !exists && relation.model && relation.type ) { + this._reverseRelations.push( relation ); + + if ( !relation.model.prototype.relations ) { + relation.model.prototype.relations = []; + } + relation.model.prototype.relations.push( relation ); + + this.retroFitRelation( relation ); + } + }, + + /** + * Add a 'relation' to all existing instances of 'relation.model' in the store + * @param {object} relation + */ + retroFitRelation: function( relation ) { + var coll = this.getCollection( relation.model ); + coll.each( function( model ) { + new relation.type( model, relation ); + }, this); + }, + + /** + * Find the Store's collection for a certain type of model. + * @param {Backbone.RelationalModel} model + * @return {Backbone.Collection} A collection if found (or applicable for 'model'), or null + */ + getCollection: function( model ) { + var coll = _.detect( this._collections, function( c ) { + // Check if model is the type itself (a ref to the constructor), or is of type c.model + return model === c.model || model.constructor === c.model; + }); + + if ( !coll ) { + coll = this._createCollection( model ); + } + + return coll; + }, + + /** + * Find a type on the global object by name. Splits name on dots. + * @param {String} name + * @return {Object} + */ + getObjectByName: function( name ) { + var type = _.reduce( name.split( '.' ), function( memo, val ) { + return memo[ val ]; + }, exports); + return type !== exports ? type: null; + }, + + _createCollection: function( type ) { + var coll; + + // If 'type' is an instance, take it's constructor + if ( type instanceof Backbone.RelationalModel ) { + type = type.constructor; + } + + // Type should inherit from Backbone.RelationalModel. + if ( type.prototype instanceof Backbone.RelationalModel.prototype.constructor ) { + coll = new Backbone.Collection(); + coll.model = type; + + this._collections.push( coll ); + } + + return coll; + }, + + /** + * Find an id + * @param type + * @param {String|Number|Object|Backbone.RelationalModel} item + */ + resolveIdForItem: function( type, item ) { + var id = _.isString( item ) || _.isNumber( item ) ? item : null; + + if ( id == null ) { + if ( item instanceof Backbone.RelationalModel ) { + id = item.id; + } + else if ( _.isObject( item ) ) { + id = item[ type.prototype.idAttribute ]; + } + } + + return id; + }, + + /** + * + * @param type + * @param {String|Number|Object|Backbone.RelationalModel} item + */ + find: function( type, item ) { + var id = this.resolveIdForItem( type, item ); + var coll = this.getCollection( type ); + return coll && coll.get( id ); + }, + + /** + * Add a 'model' to it's appropriate collection. Retain the original contents of 'model.collection'. + * @param {Backbone.RelationalModel} model + */ + register: function( model ) { + var modelColl = model.collection; + var coll = this.getCollection( model ); + coll && coll.add( model ); + model.bind( 'destroy', this.unregister, this ); + model.collection = modelColl; + }, + + /** + * Explicitly update a model's id in it's store collection + * @param {Backbone.RelationalModel} model + */ + update: function( model ) { + var coll = this.getCollection( model ); + coll._onModelEvent( 'change:' + model.idAttribute, model, coll ); + }, + + /** + * Remove a 'model' from the store. + * @param {Backbone.RelationalModel} model + */ + unregister: function( model ) { + model.unbind( 'destroy', this.unregister ); + var coll = this.getCollection( model ); + coll && coll.remove( model ); + } + }); + Backbone.Relational.store = new Backbone.Store(); + + /** + * The main Relation class, from which 'HasOne' and 'HasMany' inherit. Internally, 'relational:<key>' events + * are used to regulate addition and removal of models from relations. + * + * @param {Backbone.RelationalModel} instance + * @param {object} options + * @param {string} options.key + * @param {Backbone.RelationalModel.constructor} options.relatedModel + * @param {Boolean|String} [options.includeInJSON=true] Serialize the given attribute for related model(s)' in toJSON, or just their ids. + * @param {Boolean} [options.createModels=true] Create objects from the contents of keys if the object is not found in Backbone.store. + * @param {object} [options.reverseRelation] Specify a bi-directional relation. If provided, Relation will reciprocate + * the relation to the 'relatedModel'. Required and optional properties match 'options', except that it also needs + * {Backbone.Relation|String} type ('HasOne' or 'HasMany'). + */ + Backbone.Relation = function( instance, options ) { + this.instance = instance; + // Make sure 'options' is sane, and fill with defaults from subclasses and this object's prototype + options = ( typeof options === 'object' && options ) || {}; + this.reverseRelation = _.defaults( options.reverseRelation || {}, this.options.reverseRelation ); + this.reverseRelation.type = !_.isString( this.reverseRelation.type ) ? this.reverseRelation.type : + Backbone[ this.reverseRelation.type ] || Backbone.Relational.store.getObjectByName( this.reverseRelation.type ); + this.model = options.model || this.instance.constructor; + this.options = _.defaults( options, this.options, Backbone.Relation.prototype.options ); + + this.key = this.options.key; + this.keySource = this.options.keySource || this.key; + this.keyDestination = this.options.keyDestination || this.options.keySource || this.key; + + // 'exports' should be the global object where 'relatedModel' can be found on if given as a string. + this.relatedModel = this.options.relatedModel; + if ( _.isString( this.relatedModel ) ) { + this.relatedModel = Backbone.Relational.store.getObjectByName( this.relatedModel ); + } + + if ( !this.checkPreconditions() ) { + return false; + } + + if ( instance ) { + this.keyContents = this.instance.get( this.keySource ); + + // Explicitly clear 'keySource', to prevent a leaky abstraction if 'keySource' differs from 'key'. + if ( this.key !== this.keySource ) { + this.instance.unset( this.keySource, { silent: true } ); + } + + // Add this Relation to instance._relations + this.instance._relations.push( this ); + } + + // Add the reverse relation on 'relatedModel' to the store's reverseRelations + if ( !this.options.isAutoRelation && this.reverseRelation.type && this.reverseRelation.key ) { + Backbone.Relational.store.addReverseRelation( _.defaults( { + isAutoRelation: true, + model: this.relatedModel, + relatedModel: this.model, + reverseRelation: this.options // current relation is the 'reverseRelation' for it's own reverseRelation + }, + this.reverseRelation // Take further properties from this.reverseRelation (type, key, etc.) + ) ); + } + + _.bindAll( this, '_modelRemovedFromCollection', '_relatedModelAdded', '_relatedModelRemoved' ); + + if( instance ) { + this.initialize(); + + // When a model in the store is destroyed, check if it is 'this.instance'. + Backbone.Relational.store.getCollection( this.instance ) + .bind( 'relational:remove', this._modelRemovedFromCollection ); + + // When 'relatedModel' are created or destroyed, check if it affects this relation. + Backbone.Relational.store.getCollection( this.relatedModel ) + .bind( 'relational:add', this._relatedModelAdded ) + .bind( 'relational:remove', this._relatedModelRemoved ); + } + }; + // Fix inheritance :\ + Backbone.Relation.extend = Backbone.Model.extend; + // Set up all inheritable **Backbone.Relation** properties and methods. + _.extend( Backbone.Relation.prototype, Backbone.Events, Backbone.Semaphore, { + options: { + createModels: true, + includeInJSON: true, + isAutoRelation: false + }, + + instance: null, + key: null, + keyContents: null, + relatedModel: null, + reverseRelation: null, + related: null, + + _relatedModelAdded: function( model, coll, options ) { + // Allow 'model' to set up it's relations, before calling 'tryAddRelated' + // (which can result in a call to 'addRelated' on a relation of 'model') + var dit = this; + model.queue( function() { + dit.tryAddRelated( model, options ); + }); + }, + + _relatedModelRemoved: function( model, coll, options ) { + this.removeRelated( model, options ); + }, + + _modelRemovedFromCollection: function( model ) { + if ( model === this.instance ) { + this.destroy(); + } + }, + + /** + * Check several pre-conditions. + * @return {Boolean} True if pre-conditions are satisfied, false if they're not. + */ + checkPreconditions: function() { + var i = this.instance, + k = this.key, + m = this.model, + rm = this.relatedModel, + warn = Backbone.Relational.showWarnings && typeof console !== 'undefined'; + + if ( !m || !k || !rm ) { + warn && console.warn( 'Relation=%o; no model, key or relatedModel (%o, %o, %o)', this, m, k, rm ); + return false; + } + // Check if the type in 'relatedModel' inherits from Backbone.RelationalModel + if ( !( m.prototype instanceof Backbone.RelationalModel.prototype.constructor ) ) { + warn && console.warn( 'Relation=%o; model does not inherit from Backbone.RelationalModel (%o)', this, i ); + return false; + } + // Check if the type in 'relatedModel' inherits from Backbone.RelationalModel + if ( !( rm.prototype instanceof Backbone.RelationalModel.prototype.constructor ) ) { + warn && console.warn( 'Relation=%o; relatedModel does not inherit from Backbone.RelationalModel (%o)', this, rm ); + return false; + } + // Check if this is not a HasMany, and the reverse relation is HasMany as well + if ( this instanceof Backbone.HasMany && this.reverseRelation.type === Backbone.HasMany.prototype.constructor ) { + warn && console.warn( 'Relation=%o; relation is a HasMany, and the reverseRelation is HasMany as well.', this ); + return false; + } + + // Check if we're not attempting to create a duplicate relationship + if( i && i._relations.length ) { + var exists = _.any( i._relations, function( rel ) { + var hasReverseRelation = this.reverseRelation.key && rel.reverseRelation.key; + return rel.relatedModel === rm && rel.key === k && + ( !hasReverseRelation || this.reverseRelation.key === rel.reverseRelation.key ); + }, this ); + + if ( exists ) { + warn && console.warn( 'Relation=%o between instance=%o.%s and relatedModel=%o.%s already exists', + this, i, k, rm, this.reverseRelation.key ); + return false; + } + } + + return true; + }, + + /** + * Set the related model(s) for this relation + * @param {Backbone.Mode|Backbone.Collection} related + * @param {Object} [options] + */ + setRelated: function( related, options ) { + this.related = related; + + this.instance.acquire(); + this.instance.set( this.key, related, _.defaults( options || {}, { silent: true } ) ); + this.instance.release(); + }, + + createModel: function( item ) { + if ( this.options.createModels && typeof( item ) === 'object' ) { + return new this.relatedModel( item ); + } + }, + + /** + * Determine if a relation (on a different RelationalModel) is the reverse + * relation of the current one. + * @param {Backbone.Relation} relation + * @return {Boolean} + */ + _isReverseRelation: function( relation ) { + if ( relation.instance instanceof this.relatedModel && this.reverseRelation.key === relation.key && + this.key === relation.reverseRelation.key ) { + return true; + } + return false; + }, + + /** + * Get the reverse relations (pointing back to 'this.key' on 'this.instance') for the currently related model(s). + * @param {Backbone.RelationalModel} [model] Get the reverse relations for a specific model. + * If not specified, 'this.related' is used. + * @return {Backbone.Relation[]} + */ + getReverseRelations: function( model ) { + var reverseRelations = []; + // Iterate over 'model', 'this.related.models' (if this.related is a Backbone.Collection), or wrap 'this.related' in an array. + var models = !_.isUndefined( model ) ? [ model ] : this.related && ( this.related.models || [ this.related ] ); + _.each( models , function( related ) { + _.each( related.getRelations(), function( relation ) { + if ( this._isReverseRelation( relation ) ) { + reverseRelations.push( relation ); + } + }, this ); + }, this ); + + return reverseRelations; + }, + + /** + * Rename options.silent to options.silentChange, so events propagate properly. + * (for example in HasMany, from 'addRelated'->'handleAddition') + * @param {Object} [options] + * @return {Object} + */ + sanitizeOptions: function( options ) { + options = options ? _.clone( options ) : {}; + if ( options.silent ) { + options = _.extend( {}, options, { silentChange: true } ); + delete options.silent; + } + return options; + }, + + /** + * Rename options.silentChange to options.silent, so events are silenced as intended in Backbone's + * original functions. + * @param {Object} [options] + * @return {Object} + */ + unsanitizeOptions: function( options ) { + options = options ? _.clone( options ) : {}; + if ( options.silentChange ) { + options = _.extend( {}, options, { silent: true } ); + delete options.silentChange; + } + return options; + }, + + // Cleanup. Get reverse relation, call removeRelated on each. + destroy: function() { + Backbone.Relational.store.getCollection( this.instance ) + .unbind( 'relational:remove', this._modelRemovedFromCollection ); + + Backbone.Relational.store.getCollection( this.relatedModel ) + .unbind( 'relational:add', this._relatedModelAdded ) + .unbind( 'relational:remove', this._relatedModelRemoved ); + + _.each( this.getReverseRelations(), function( relation ) { + relation.removeRelated( this.instance ); + }, this ); + } + }); + + Backbone.HasOne = Backbone.Relation.extend({ + options: { + reverseRelation: { type: 'HasMany' } + }, + + initialize: function() { + _.bindAll( this, 'onChange' ); + + this.instance.bind( 'relational:change:' + this.key, this.onChange ); + + var model = this.findRelated( { silent: true } ); + this.setRelated( model ); + + // Notify new 'related' object of the new relation. + var dit = this; + _.each( dit.getReverseRelations(), function( relation ) { + relation.addRelated( dit.instance ); + } ); + }, + + findRelated: function( options ) { + var item = this.keyContents; + var model = null; + + if ( item instanceof this.relatedModel ) { + model = item; + } + else if ( item ) { + // Try to find an instance of the appropriate 'relatedModel' in the store, or create it + model = Backbone.Relational.store.find( this.relatedModel, item ); + + if ( model && _.isObject( item ) ) { + model.set( item, options ); + } + else if ( !model ) { + model = this.createModel( item ); + } + } + + return model; + }, + + /** + * If the key is changed, notify old & new reverse relations and initialize the new relation + */ + onChange: function( model, attr, options ) { + // Don't accept recursive calls to onChange (like onChange->findRelated->createModel->initializeRelations->addRelated->onChange) + if ( this.isLocked() ) { + return; + } + this.acquire(); + options = this.sanitizeOptions( options ); + + // 'options._related' is set by 'addRelated'/'removeRelated'. If it is set, the change + // is the result of a call from a relation. If it's not, the change is the result of + // a 'set' call on this.instance. + var changed = _.isUndefined( options._related ); + var oldRelated = changed ? this.related : options._related; + + if ( changed ) { + this.keyContents = attr; + + // Set new 'related' + if ( attr instanceof this.relatedModel ) { + this.related = attr; + } + else if ( attr ) { + var related = this.findRelated( options ); + this.setRelated( related ); + } + else { + this.setRelated( null ); + } + } + + // Notify old 'related' object of the terminated relation + if ( oldRelated && this.related !== oldRelated ) { + _.each( this.getReverseRelations( oldRelated ), function( relation ) { + relation.removeRelated( this.instance, options ); + }, this ); + } + + // Notify new 'related' object of the new relation. Note we do re-apply even if this.related is oldRelated; + // that can be necessary for bi-directional relations if 'this.instance' was created after 'this.related'. + // In that case, 'this.instance' will already know 'this.related', but the reverse might not exist yet. + _.each( this.getReverseRelations(), function( relation ) { + relation.addRelated( this.instance, options ); + }, this); + + // Fire the 'update:<key>' event if 'related' was updated + if ( !options.silentChange && this.related !== oldRelated ) { + var dit = this; + Backbone.Relational.eventQueue.add( function() { + dit.instance.trigger( 'update:' + dit.key, dit.instance, dit.related, options ); + }); + } + this.release(); + }, + + /** + * If a new 'this.relatedModel' appears in the 'store', try to match it to the last set 'keyContents' + */ + tryAddRelated: function( model, options ) { + if ( this.related ) { + return; + } + options = this.sanitizeOptions( options ); + + var item = this.keyContents; + if ( item ) { + var id = Backbone.Relational.store.resolveIdForItem( this.relatedModel, item ); + if ( model.id === id ) { + this.addRelated( model, options ); + } + } + }, + + addRelated: function( model, options ) { + if ( model !== this.related ) { + var oldRelated = this.related || null; + this.setRelated( model ); + this.onChange( this.instance, model, { _related: oldRelated } ); + } + }, + + removeRelated: function( model, options ) { + if ( !this.related ) { + return; + } + + if ( model === this.related ) { + var oldRelated = this.related || null; + this.setRelated( null ); + this.onChange( this.instance, model, { _related: oldRelated } ); + } + } + }); + + Backbone.HasMany = Backbone.Relation.extend({ + collectionType: null, + + options: { + reverseRelation: { type: 'HasOne' }, + collectionType: Backbone.Collection, + collectionKey: true, + collectionOptions: {} + }, + + initialize: function() { + _.bindAll( this, 'onChange', 'handleAddition', 'handleRemoval', 'handleReset' ); + this.instance.bind( 'relational:change:' + this.key, this.onChange ); + + // Handle a custom 'collectionType' + this.collectionType = this.options.collectionType; + if ( _( this.collectionType ).isString() ) { + this.collectionType = Backbone.Relational.store.getObjectByName( this.collectionType ); + } + if ( !this.collectionType.prototype instanceof Backbone.Collection.prototype.constructor ){ + throw new Error( 'collectionType must inherit from Backbone.Collection' ); + } + + // Handle cases where a model/relation is created with a collection passed straight into 'attributes' + if ( this.keyContents instanceof Backbone.Collection ) { + this.setRelated( this._prepareCollection( this.keyContents ) ); + } + else { + this.setRelated( this._prepareCollection() ); + } + + this.findRelated( { silent: true } ); + }, + + _getCollectionOptions: function() { + return _.isFunction( this.options.collectionOptions ) ? + this.options.collectionOptions( this.instance ) : + this.options.collectionOptions; + }, + + /** + * Bind events and setup collectionKeys for a collection that is to be used as the backing store for a HasMany. + * If no 'collection' is supplied, a new collection will be created of the specified 'collectionType' option. + * @param {Backbone.Collection} [collection] + */ + _prepareCollection: function( collection ) { + if ( this.related ) { + this.related + .unbind( 'relational:add', this.handleAddition ) + .unbind( 'relational:remove', this.handleRemoval ) + .unbind( 'relational:reset', this.handleReset ) + } + + if ( !collection || !( collection instanceof Backbone.Collection ) ) { + collection = new this.collectionType( [], this._getCollectionOptions() ); + } + + collection.model = this.relatedModel; + + if ( this.options.collectionKey ) { + var key = this.options.collectionKey === true ? this.options.reverseRelation.key : this.options.collectionKey; + + if (collection[ key ] && collection[ key ] !== this.instance ) { + if ( Backbone.Relational.showWarnings && typeof console !== 'undefined' ) { + console.warn( 'Relation=%o; collectionKey=%s already exists on collection=%o', this, key, this.options.collectionKey ); + } + } + else if (key) { + collection[ key ] = this.instance; + } + } + + collection + .bind( 'relational:add', this.handleAddition ) + .bind( 'relational:remove', this.handleRemoval ) + .bind( 'relational:reset', this.handleReset ); + + return collection; + }, + + findRelated: function( options ) { + if ( this.keyContents ) { + var models = []; + + if ( this.keyContents instanceof Backbone.Collection ) { + models = this.keyContents.models; + } + else { + // Handle cases the an API/user supplies just an Object/id instead of an Array + this.keyContents = _.isArray( this.keyContents ) ? this.keyContents : [ this.keyContents ]; + + // Try to find instances of the appropriate 'relatedModel' in the store + _.each( this.keyContents, function( item ) { + var model = Backbone.Relational.store.find( this.relatedModel, item ); + + if ( model && _.isObject( item ) ) { + model.set( item, options ); + } + else if ( !model ) { + model = this.createModel( item ); + } + + if ( model && !this.related.getByCid( model ) && !this.related.get( model ) ) { + models.push( model ); + } + }, this ); + } + + // Add all found 'models' in on go, so 'add' will only be called once (and thus 'sort', etc.) + if ( models.length ) { + options = this.unsanitizeOptions( options ); + this.related.add( models, options ); + } + } + }, + + /** + * If the key is changed, notify old & new reverse relations and initialize the new relation + */ + onChange: function( model, attr, options ) { + options = this.sanitizeOptions( options ); + this.keyContents = attr; + + // Notify old 'related' object of the terminated relation + _.each( this.getReverseRelations(), function( relation ) { + relation.removeRelated( this.instance, options ); + }, this ); + + // Replace 'this.related' by 'attr' if it is a Backbone.Collection + if ( attr instanceof Backbone.Collection ) { + this._prepareCollection( attr ); + this.related = attr; + } + // Otherwise, 'attr' should be an array of related object ids. + // Re-use the current 'this.related' if it is a Backbone.Collection, and remove any current entries. + // Otherwise, create a new collection. + else { + var coll; + + if ( this.related instanceof Backbone.Collection ) { + coll = this.related; + coll.reset( [], { silent: true } ); + } + else { + coll = this._prepareCollection(); + } + + this.setRelated( coll ); + this.findRelated( options ); + } + + // Notify new 'related' object of the new relation + _.each( this.getReverseRelations(), function( relation ) { + relation.addRelated( this.instance, options ); + }, this ); + + var dit = this; + Backbone.Relational.eventQueue.add( function() { + !options.silentChange && dit.instance.trigger( 'update:' + dit.key, dit.instance, dit.related, options ); + }); + }, + + tryAddRelated: function( model, options ) { + options = this.sanitizeOptions( options ); + if ( !this.related.getByCid( model ) && !this.related.get( model ) ) { + // Check if this new model was specified in 'this.keyContents' + var item = _.any( this.keyContents, function( item ) { + var id = Backbone.Relational.store.resolveIdForItem( this.relatedModel, item ); + return id && id === model.id; + }, this ); + + if ( item ) { + this.related.add( model, options ); + } + } + }, + + /** + * When a model is added to a 'HasMany', trigger 'add' on 'this.instance' and notify reverse relations. + * (should be 'HasOne', must set 'this.instance' as their related). + */ + handleAddition: function( model, coll, options ) { + //console.debug('handleAddition called; args=%o', arguments); + // Make sure the model is in fact a valid model before continuing. + // (it can be invalid as a result of failing validation in Backbone.Collection._prepareModel) + if( !( model instanceof Backbone.Model ) ) { + return; + } + + options = this.sanitizeOptions( options ); + + _.each( this.getReverseRelations( model ), function( relation ) { + relation.addRelated( this.instance, options ); + }, this ); + + // Only trigger 'add' once the newly added model is initialized (so, has it's relations set up) + var dit = this; + Backbone.Relational.eventQueue.add( function() { + !options.silentChange && dit.instance.trigger( 'add:' + dit.key, model, dit.related, options ); + }); + }, + + /** + * When a model is removed from a 'HasMany', trigger 'remove' on 'this.instance' and notify reverse relations. + * (should be 'HasOne', which should be nullified) + */ + handleRemoval: function( model, coll, options ) { + //console.debug('handleRemoval called; args=%o', arguments); + if( !( model instanceof Backbone.Model ) ) { + return; + } + + options = this.sanitizeOptions( options ); + + _.each( this.getReverseRelations( model ), function( relation ) { + relation.removeRelated( this.instance, options ); + }, this ); + + var dit = this; + Backbone.Relational.eventQueue.add( function() { + !options.silentChange && dit.instance.trigger( 'remove:' + dit.key, model, dit.related, options ); + }); + }, + + handleReset: function( coll, options ) { + options = this.sanitizeOptions( options ); + + var dit = this; + Backbone.Relational.eventQueue.add( function() { + !options.silentChange && dit.instance.trigger( 'reset:' + dit.key, dit.related, options ); + }); + }, + + addRelated: function( model, options ) { + var dit = this; + options = this.unsanitizeOptions( options ); + model.queue( function() { // Queued to avoid errors for adding 'model' to the 'this.related' set twice + if ( dit.related && !dit.related.getByCid( model ) && !dit.related.get( model ) ) { + dit.related.add( model, options ); + } + }); + }, + + removeRelated: function( model, options ) { + options = this.unsanitizeOptions( options ); + if ( this.related.getByCid( model ) || this.related.get( model ) ) { + this.related.remove( model, options ); + } + } + }); + + /** + * A type of Backbone.Model that also maintains relations to other models and collections. + * New events when compared to the original: + * - 'add:<key>' (model, related collection, options) + * - 'remove:<key>' (model, related collection, options) + * - 'update:<key>' (model, related model or collection, options) + */ + Backbone.RelationalModel = Backbone.Model.extend({ + relations: null, // Relation descriptions on the prototype + _relations: null, // Relation instances + _isInitialized: false, + _deferProcessing: false, + _queue: null, + + constructor: function( attributes, options ) { + // Nasty hack, for cases like 'model.get( <HasMany key> ).add( item )'. + // Defer 'processQueue', so that when 'Relation.createModels' is used we: + // a) Survive 'Backbone.Collection.add'; this takes care we won't error on "can't add model to a set twice" + // (by creating a model from properties, having the model add itself to the collection via one of + // it's relations, then trying to add it to the collection). + // b) Trigger 'HasMany' collection events only after the model is really fully set up. + // Example that triggers both a and b: "p.get('jobs').add( { company: c, person: p } )". + var dit = this; + if ( options && options.collection ) { + this._deferProcessing = true; + + var processQueue = function( model ) { + if ( model === dit ) { + dit._deferProcessing = false; + dit.processQueue(); + options.collection.unbind( 'relational:add', processQueue ); + } + }; + options.collection.bind( 'relational:add', processQueue ); + + // So we do process the queue eventually, regardless of whether this model really gets added to 'options.collection'. + _.defer( function() { + processQueue( dit ); + }); + } + + this._queue = new Backbone.BlockingQueue(); + this._queue.block(); + Backbone.Relational.eventQueue.block(); + + Backbone.Model.prototype.constructor.apply( this, arguments ); + + // Try to run the global queue holding external events + Backbone.Relational.eventQueue.unblock(); + }, + + /** + * Override 'trigger' to queue 'change' and 'change:*' events + */ + trigger: function( eventName ) { + if ( eventName.length > 5 && 'change' === eventName.substr( 0, 6 ) ) { + var dit = this, args = arguments; + Backbone.Relational.eventQueue.add( function() { + Backbone.Model.prototype.trigger.apply( dit, args ); + }); + } + else { + Backbone.Model.prototype.trigger.apply( this, arguments ); + } + + return this; + }, + + /** + * Initialize Relations present in this.relations; determine the type (HasOne/HasMany), then creates a new instance. + * Invoked in the first call so 'set' (which is made from the Backbone.Model constructor). + */ + initializeRelations: function() { + this.acquire(); // Setting up relations often also involve calls to 'set', and we only want to enter this function once + this._relations = []; + + _.each( this.relations, function( rel ) { + var type = !_.isString( rel.type ) ? rel.type : Backbone[ rel.type ] || Backbone.Relational.store.getObjectByName( rel.type ); + if ( type && type.prototype instanceof Backbone.Relation.prototype.constructor ) { + new type( this, rel ); // Also pushes the new Relation into _relations + } + else { + Backbone.Relational.showWarnings && typeof console !== 'undefined' && console.warn( 'Relation=%o; missing or invalid type!', rel ); + } + }, this ); + + this._isInitialized = true; + this.release(); + this.processQueue(); + }, + + /** + * When new values are set, notify this model's relations (also if options.silent is set). + * (Relation.setRelated locks this model before calling 'set' on it to prevent loops) + */ + updateRelations: function( options ) { + if( this._isInitialized && !this.isLocked() ) { + _.each( this._relations, function( rel ) { + var val = this.attributes[ rel.key ]; + if ( rel.related !== val ) { + this.trigger('relational:change:' + rel.key, this, val, options || {} ); + } + }, this ); + } + }, + + /** + * Either add to the queue (if we're not initialized yet), or execute right away. + */ + queue: function( func ) { + this._queue.add( func ); + }, + + /** + * Process _queue + */ + processQueue: function() { + if ( this._isInitialized && !this._deferProcessing && this._queue.isBlocked() ) { + this._queue.unblock(); + } + }, + + /** + * Get a specific relation. + * @param key {string} The relation key to look for. + * @return {Backbone.Relation} An instance of 'Backbone.Relation', if a relation was found for 'key', or null. + */ + getRelation: function( key ) { + return _.detect( this._relations, function( rel ) { + if ( rel.key === key ) { + return true; + } + }, this ); + }, + + /** + * Get all of the created relations. + * @return {Backbone.Relation[]} + */ + getRelations: function() { + return this._relations; + }, + + /** + * Retrieve related objects. + * @param key {string} The relation key to fetch models for. + * @param options {object} Options for 'Backbone.Model.fetch' and 'Backbone.sync'. + * @return {jQuery.when[]} An array of request objects + */ + fetchRelated: function( key, options ) { + options || ( options = {} ); + var setUrl, + requests = [], + rel = this.getRelation( key ), + keyContents = rel && rel.keyContents, + toFetch = keyContents && _.select( _.isArray( keyContents ) ? keyContents : [ keyContents ], function( item ) { + var id = Backbone.Relational.store.resolveIdForItem( rel.relatedModel, item ); + return id && !Backbone.Relational.store.find( rel.relatedModel, id ); + }, this ); + + if ( toFetch && toFetch.length ) { + // Create a model for each entry in 'keyContents' that is to be fetched + var models = _.map( toFetch, function( item ) { + var model; + + if ( typeof( item ) === 'object' ) { + model = new rel.relatedModel( item ); + } + else { + var attrs = {}; + attrs[ rel.relatedModel.prototype.idAttribute ] = item; + model = new rel.relatedModel( attrs ); + } + + return model; + }, this ); + + // Try if the 'collection' can provide a url to fetch a set of models in one request. + if ( rel.related instanceof Backbone.Collection && _.isFunction( rel.related.url ) ) { + setUrl = rel.related.url( models ); + } + + // An assumption is that when 'Backbone.Collection.url' is a function, it can handle building of set urls. + // To make sure it can, test if the url we got by supplying a list of models to fetch is different from + // the one supplied for the default fetch action (without args to 'url'). + if ( setUrl && setUrl !== rel.related.url() ) { + var opts = _.defaults( + { + error: function() { + var args = arguments; + _.each( models, function( model ) { + model.trigger( 'destroy', model, model.collection, options ); + options.error && options.error.apply( model, args ); + }); + }, + url: setUrl + }, + options, + { add: true } + ); + + requests = [ rel.related.fetch( opts ) ]; + } + else { + requests = _.map( models, function( model ) { + var opts = _.defaults( + { + error: function() { + model.trigger( 'destroy', model, model.collection, options ); + options.error && options.error.apply( model, arguments ); + } + }, + options + ); + return model.fetch( opts ); + }, this ); + } + } + + return requests; + }, + + set: function( key, value, options ) { + Backbone.Relational.eventQueue.block(); + + // Duplicate backbone's behavior to allow separate key/value parameters, instead of a single 'attributes' object + var attributes; + if (_.isObject( key ) || key == null) { + attributes = key; + options = value; + } + else { + attributes = {}; + attributes[ key ] = value; + } + + var result = Backbone.Model.prototype.set.apply( this, arguments ); + + // 'set' is called quite late in 'Backbone.Model.prototype.constructor', but before 'initialize'. + // Ideal place to set up relations :) + if ( !this._isInitialized && !this.isLocked() ) { + Backbone.Relational.store.register( this ); + this.initializeRelations(); + } + // Update the 'idAttribute' in Backbone.store if; we don't want it to miss an 'id' update due to {silent:true} + else if ( attributes && this.idAttribute in attributes ) { + Backbone.Relational.store.update( this ); + } + + if ( attributes ) { + this.updateRelations( options ); + } + + // Try to run the global queue holding external events + Backbone.Relational.eventQueue.unblock(); + + return result; + }, + + unset: function( attribute, options ) { + Backbone.Relational.eventQueue.block(); + + var result = Backbone.Model.prototype.unset.apply( this, arguments ); + this.updateRelations( options ); + + // Try to run the global queue holding external events + Backbone.Relational.eventQueue.unblock(); + + return result; + }, + + clear: function( options ) { + Backbone.Relational.eventQueue.block(); + + var result = Backbone.Model.prototype.clear.apply( this, arguments ); + this.updateRelations( options ); + + // Try to run the global queue holding external events + Backbone.Relational.eventQueue.unblock(); + + return result; + }, + + /** + * Override 'change', so the change will only execute after 'set' has finised (relations are updated), + * and 'previousAttributes' will be available when the event is fired. + */ + change: function( options ) { + var dit = this, args = arguments; + Backbone.Relational.eventQueue.add( function() { + Backbone.Model.prototype.change.apply( dit, args ); + }); + }, + + clone: function() { + var attributes = _.clone( this.attributes ); + if ( !_.isUndefined( attributes[ this.idAttribute ] ) ) { + attributes[ this.idAttribute ] = null; + } + + _.each( this.getRelations(), function( rel ) { + delete attributes[ rel.key ]; + }); + + return new this.constructor( attributes ); + }, + + /** + * Convert relations to JSON, omits them when required + */ + toJSON: function() { + // If this Model has already been fully serialized in this branch once, return to avoid loops + if ( this.isLocked() ) { + return this.id; + } + + this.acquire(); + var json = Backbone.Model.prototype.toJSON.call( this ); + + _.each( this._relations, function( rel ) { + var value = json[ rel.key ]; + + if ( rel.options.includeInJSON === true && value && _.isFunction( value.toJSON ) ) { + json[ rel.keyDestination ] = value.toJSON(); + } + else if ( _.isString( rel.options.includeInJSON ) ) { + if ( value instanceof Backbone.Collection ) { + json[ rel.keyDestination ] = value.pluck( rel.options.includeInJSON ); + } + else if ( value instanceof Backbone.Model ) { + json[ rel.keyDestination ] = value.get( rel.options.includeInJSON ); + } + } + else { + delete json[ rel.key ]; + } + + if ( rel.keyDestination !== rel.key ) { + delete json[ rel.key ]; + } + }, this ); + + this.release(); + return json; + } + }); + _.extend( Backbone.RelationalModel.prototype, Backbone.Semaphore ); + + /** + * Override Backbone.Collection.add, so objects fetched from the server multiple times will + * update the existing Model. Also, trigger 'relational:add'. + */ + var add = Backbone.Collection.prototype.__add = Backbone.Collection.prototype.add; + Backbone.Collection.prototype.add = function( models, options ) { + options || (options = {}); + if ( !_.isArray( models ) ) { + models = [ models ]; + } + + var modelsToAdd = []; + + //console.debug( 'calling add on coll=%o; model=%o, options=%o', this, models, options ); + _.each( models, function( model ) { + if ( !( model instanceof Backbone.Model ) ) { + // Try to find 'model' in Backbone.store. If it already exists, set the new properties on it. + var existingModel = Backbone.Relational.store.find( this.model, model[ this.model.prototype.idAttribute ] ); + if ( existingModel ) { + existingModel.set( existingModel.parse ? existingModel.parse( model ) : model, options ); + model = existingModel; + } + else { + model = Backbone.Collection.prototype._prepareModel.call( this, model, options ); + } + } + + if ( model instanceof Backbone.Model && !this.get( model ) && !this.getByCid( model ) ) { + modelsToAdd.push( model ); + } + }, this ); + + + // Add 'models' in a single batch, so the original add will only be called once (and thus 'sort', etc). + if ( modelsToAdd.length ) { + add.call( this, modelsToAdd, options ); + + _.each( modelsToAdd, function( model ) { + this.trigger('relational:add', model, this, options); + }, this ); + } + + return this; + }; + + /** + * Override 'Backbone.Collection.remove' to trigger 'relational:remove'. + */ + var remove = Backbone.Collection.prototype.__remove = Backbone.Collection.prototype.remove; + Backbone.Collection.prototype.remove = function( models, options ) { + options || (options = {}); + if (!_.isArray( models ) ) { + models = [ models ]; + } + + //console.debug('calling remove on coll=%o; models=%o, options=%o', this, models, options ); + _.each( models, function( model ) { + model = this.getByCid( model ) || this.get( model ); + + if ( model instanceof Backbone.Model ) { + remove.call( this, model, options ); + this.trigger('relational:remove', model, this, options); + } + }, this ); + + return this; + }; + + /** + * Override 'Backbone.Collection.reset' to trigger 'relational:reset'. + */ + var reset = Backbone.Collection.prototype.__reset = Backbone.Collection.prototype.reset; + Backbone.Collection.prototype.reset = function( models, options ) { + reset.call( this, models, options ); + this.trigger( 'relational:reset', models, options ); + + return this; + }; + + /** + * Override 'Backbone.Collection.trigger' so 'add', 'remove' and 'reset' events are queued until relations + * are ready. + */ + var trigger = Backbone.Collection.prototype.__trigger = Backbone.Collection.prototype.trigger; + Backbone.Collection.prototype.trigger = function( eventName ) { + if ( eventName === 'add' || eventName === 'remove' || eventName === 'reset' ) { + var dit = this, args = arguments; + Backbone.Relational.eventQueue.add( function() { + trigger.apply( dit, args ); + }); + } + else { + trigger.apply( this, arguments ); + } + + return this; + }; + + // Override .extend() to check for reverseRelations to initialize. + Backbone.RelationalModel.extend = function( protoProps, classProps ) { + var child = Backbone.Model.extend.apply( this, arguments ); + + var relations = ( protoProps && protoProps.relations ) || []; + _.each( relations, function( rel ) { + if( rel.reverseRelation ) { + rel.model = child; + + var preInitialize = true; + if ( _.isString( rel.relatedModel ) ) { + /** + * The related model might not be defined for two reasons + * 1. it never gets defined, e.g. a typo + * 2. it is related to itself + * In neither of these cases do we need to pre-initialize reverse relations. + */ + var relatedModel = Backbone.Relational.store.getObjectByName( rel.relatedModel ); + preInitialize = relatedModel && ( relatedModel.prototype instanceof Backbone.RelationalModel.prototype.constructor ); + } + + var type = !_.isString( rel.type ) ? rel.type : Backbone[ rel.type ] || Backbone.Relational.store.getObjectByName( rel.type ); + if ( preInitialize && type && type.prototype instanceof Backbone.Relation.prototype.constructor ) { + new type( null, rel ); + } + } + }); + + return child; + }; + +})(); diff -r bf88ce609370a7829337dad758fafe388b3fd117 -r 0a957e499a3c9b7ba11f88d337e4878260d73d6d static/scripts/packed/libs/backbone-relational.js --- /dev/null +++ b/static/scripts/packed/libs/backbone-relational.js @@ -0,0 +1,1 @@ +(function(g){var d,h,b;if(typeof window==="undefined"){d=require("underscore");h=require("backbone");b=module.exports=h}else{var d=window._;h=window.Backbone;b=window}h.Relational={showWarnings:true};h.Semaphore={_permitsAvailable:null,_permitsUsed:0,acquire:function(){if(this._permitsAvailable&&this._permitsUsed>=this._permitsAvailable){throw new Error("Max permits acquired")}else{this._permitsUsed++}},release:function(){if(this._permitsUsed===0){throw new Error("All permits released")}else{this._permitsUsed--}},isLocked:function(){return this._permitsUsed>0},setAvailablePermits:function(i){if(this._permitsUsed>i){throw new Error("Available permits cannot be less than used permits")}this._permitsAvailable=i}};h.BlockingQueue=function(){this._queue=[]};d.extend(h.BlockingQueue.prototype,h.Semaphore,{_queue:null,add:function(i){if(this.isBlocked()){this._queue.push(i)}else{i()}},process:function(){while(this._queue&&this._queue.length){this._queue.shift()()}},block:function(){this.acquire()},unblock:function(){this.release();if(!this.isBlocked()){this.process()}},isBlocked:function(){return this.isLocked()}});h.Relational.eventQueue=new h.BlockingQueue();h.Store=function(){this._collections=[];this._reverseRelations=[]};d.extend(h.Store.prototype,h.Events,{_collections:null,_reverseRelations:null,addReverseRelation:function(j){var i=d.any(this._reverseRelations,function(k){return d.all(j,function(m,l){return m===k[l]})});if(!i&&j.model&&j.type){this._reverseRelations.push(j);if(!j.model.prototype.relations){j.model.prototype.relations=[]}j.model.prototype.relations.push(j);this.retroFitRelation(j)}},retroFitRelation:function(j){var i=this.getCollection(j.model);i.each(function(k){new j.type(k,j)},this)},getCollection:function(i){var j=d.detect(this._collections,function(k){return i===k.model||i.constructor===k.model});if(!j){j=this._createCollection(i)}return j},getObjectByName:function(i){var j=d.reduce(i.split("."),function(k,l){return k[l]},b);return j!==b?j:null},_createCollection:function(j){var i;if(j instanceof h.RelationalModel){j=j.constructor}if(j.prototype instanceof h.RelationalModel.prototype.constructor){i=new h.Collection();i.model=j;this._collections.push(i)}return i},resolveIdForItem:function(i,j){var k=d.isString(j)||d.isNumber(j)?j:null;if(k==null){if(j instanceof h.RelationalModel){k=j.id}else{if(d.isObject(j)){k=j[i.prototype.idAttribute]}}}return k},find:function(j,k){var l=this.resolveIdForItem(j,k);var i=this.getCollection(j);return i&&i.get(l)},register:function(j){var i=j.collection;var k=this.getCollection(j);k&&k.add(j);j.bind("destroy",this.unregister,this);j.collection=i},update:function(i){var j=this.getCollection(i);j._onModelEvent("change:"+i.idAttribute,i,j)},unregister:function(i){i.unbind("destroy",this.unregister);var j=this.getCollection(i);j&&j.remove(i)}});h.Relational.store=new h.Store();h.Relation=function(i,j){this.instance=i;j=(typeof j==="object"&&j)||{};this.reverseRelation=d.defaults(j.reverseRelation||{},this.options.reverseRelation);this.reverseRelation.type=!d.isString(this.reverseRelation.type)?this.reverseRelation.type:h[this.reverseRelation.type]||h.Relational.store.getObjectByName(this.reverseRelation.type);this.model=j.model||this.instance.constructor;this.options=d.defaults(j,this.options,h.Relation.prototype.options);this.key=this.options.key;this.keySource=this.options.keySource||this.key;this.keyDestination=this.options.keyDestination||this.options.keySource||this.key;this.relatedModel=this.options.relatedModel;if(d.isString(this.relatedModel)){this.relatedModel=h.Relational.store.getObjectByName(this.relatedModel)}if(!this.checkPreconditions()){return false}if(i){this.keyContents=this.instance.get(this.keySource);if(this.key!==this.keySource){this.instance.unset(this.keySource,{silent:true})}this.instance._relations.push(this)}if(!this.options.isAutoRelation&&this.reverseRelation.type&&this.reverseRelation.key){h.Relational.store.addReverseRelation(d.defaults({isAutoRelation:true,model:this.relatedModel,relatedModel:this.model,reverseRelation:this.options},this.reverseRelation))}d.bindAll(this,"_modelRemovedFromCollection","_relatedModelAdded","_relatedModelRemoved");if(i){this.initialize();h.Relational.store.getCollection(this.instance).bind("relational:remove",this._modelRemovedFromCollection);h.Relational.store.getCollection(this.relatedModel).bind("relational:add",this._relatedModelAdded).bind("relational:remove",this._relatedModelRemoved)}};h.Relation.extend=h.Model.extend;d.extend(h.Relation.prototype,h.Events,h.Semaphore,{options:{createModels:true,includeInJSON:true,isAutoRelation:false},instance:null,key:null,keyContents:null,relatedModel:null,reverseRelation:null,related:null,_relatedModelAdded:function(k,l,j){var i=this;k.queue(function(){i.tryAddRelated(k,j)})},_relatedModelRemoved:function(j,k,i){this.removeRelated(j,i)},_modelRemovedFromCollection:function(i){if(i===this.instance){this.destroy()}},checkPreconditions:function(){var n=this.instance,l=this.key,j=this.model,p=this.relatedModel,q=h.Relational.showWarnings&&typeof console!=="undefined";if(!j||!l||!p){q&&console.warn("Relation=%o; no model, key or relatedModel (%o, %o, %o)",this,j,l,p);return false}if(!(j.prototype instanceof h.RelationalModel.prototype.constructor)){q&&console.warn("Relation=%o; model does not inherit from Backbone.RelationalModel (%o)",this,n);return false}if(!(p.prototype instanceof h.RelationalModel.prototype.constructor)){q&&console.warn("Relation=%o; relatedModel does not inherit from Backbone.RelationalModel (%o)",this,p);return false}if(this instanceof h.HasMany&&this.reverseRelation.type===h.HasMany.prototype.constructor){q&&console.warn("Relation=%o; relation is a HasMany, and the reverseRelation is HasMany as well.",this);return false}if(n&&n._relations.length){var o=d.any(n._relations,function(i){var k=this.reverseRelation.key&&i.reverseRelation.key;return i.relatedModel===p&&i.key===l&&(!k||this.reverseRelation.key===i.reverseRelation.key)},this);if(o){q&&console.warn("Relation=%o between instance=%o.%s and relatedModel=%o.%s already exists",this,n,l,p,this.reverseRelation.key);return false}}return true},setRelated:function(j,i){this.related=j;this.instance.acquire();this.instance.set(this.key,j,d.defaults(i||{},{silent:true}));this.instance.release()},createModel:function(i){if(this.options.createModels&&typeof(i)==="object"){return new this.relatedModel(i)}},_isReverseRelation:function(i){if(i.instance instanceof this.relatedModel&&this.reverseRelation.key===i.key&&this.key===i.reverseRelation.key){return true}return false},getReverseRelations:function(i){var j=[];var k=!d.isUndefined(i)?[i]:this.related&&(this.related.models||[this.related]);d.each(k,function(l){d.each(l.getRelations(),function(m){if(this._isReverseRelation(m)){j.push(m)}},this)},this);return j},sanitizeOptions:function(i){i=i?d.clone(i):{};if(i.silent){i=d.extend({},i,{silentChange:true});delete i.silent}return i},unsanitizeOptions:function(i){i=i?d.clone(i):{};if(i.silentChange){i=d.extend({},i,{silent:true});delete i.silentChange}return i},destroy:function(){h.Relational.store.getCollection(this.instance).unbind("relational:remove",this._modelRemovedFromCollection);h.Relational.store.getCollection(this.relatedModel).unbind("relational:add",this._relatedModelAdded).unbind("relational:remove",this._relatedModelRemoved);d.each(this.getReverseRelations(),function(i){i.removeRelated(this.instance)},this)}});h.HasOne=h.Relation.extend({options:{reverseRelation:{type:"HasMany"}},initialize:function(){d.bindAll(this,"onChange");this.instance.bind("relational:change:"+this.key,this.onChange);var j=this.findRelated({silent:true});this.setRelated(j);var i=this;d.each(i.getReverseRelations(),function(k){k.addRelated(i.instance)})},findRelated:function(j){var k=this.keyContents;var i=null;if(k instanceof this.relatedModel){i=k}else{if(k){i=h.Relational.store.find(this.relatedModel,k);if(i&&d.isObject(k)){i.set(k,j)}else{if(!i){i=this.createModel(k)}}}}return i},onChange:function(l,i,k){if(this.isLocked()){return}this.acquire();k=this.sanitizeOptions(k);var o=d.isUndefined(k._related);var m=o?this.related:k._related;if(o){this.keyContents=i;if(i instanceof this.relatedModel){this.related=i}else{if(i){var n=this.findRelated(k);this.setRelated(n)}else{this.setRelated(null)}}}if(m&&this.related!==m){d.each(this.getReverseRelations(m),function(p){p.removeRelated(this.instance,k)},this)}d.each(this.getReverseRelations(),function(p){p.addRelated(this.instance,k)},this);if(!k.silentChange&&this.related!==m){var j=this;h.Relational.eventQueue.add(function(){j.instance.trigger("update:"+j.key,j.instance,j.related,k)})}this.release()},tryAddRelated:function(j,i){if(this.related){return}i=this.sanitizeOptions(i);var k=this.keyContents;if(k){var l=h.Relational.store.resolveIdForItem(this.relatedModel,k);if(j.id===l){this.addRelated(j,i)}}},addRelated:function(j,i){if(j!==this.related){var k=this.related||null;this.setRelated(j);this.onChange(this.instance,j,{_related:k})}},removeRelated:function(j,i){if(!this.related){return}if(j===this.related){var k=this.related||null;this.setRelated(null);this.onChange(this.instance,j,{_related:k})}}});h.HasMany=h.Relation.extend({collectionType:null,options:{reverseRelation:{type:"HasOne"},collectionType:h.Collection,collectionKey:true,collectionOptions:{}},initialize:function(){d.bindAll(this,"onChange","handleAddition","handleRemoval","handleReset");this.instance.bind("relational:change:"+this.key,this.onChange);this.collectionType=this.options.collectionType;if(d(this.collectionType).isString()){this.collectionType=h.Relational.store.getObjectByName(this.collectionType)}if(!this.collectionType.prototype instanceof h.Collection.prototype.constructor){throw new Error("collectionType must inherit from Backbone.Collection")}if(this.keyContents instanceof h.Collection){this.setRelated(this._prepareCollection(this.keyContents))}else{this.setRelated(this._prepareCollection())}this.findRelated({silent:true})},_getCollectionOptions:function(){return d.isFunction(this.options.collectionOptions)?this.options.collectionOptions(this.instance):this.options.collectionOptions},_prepareCollection:function(j){if(this.related){this.related.unbind("relational:add",this.handleAddition).unbind("relational:remove",this.handleRemoval).unbind("relational:reset",this.handleReset)}if(!j||!(j instanceof h.Collection)){j=new this.collectionType([],this._getCollectionOptions())}j.model=this.relatedModel;if(this.options.collectionKey){var i=this.options.collectionKey===true?this.options.reverseRelation.key:this.options.collectionKey;if(j[i]&&j[i]!==this.instance){if(h.Relational.showWarnings&&typeof console!=="undefined"){console.warn("Relation=%o; collectionKey=%s already exists on collection=%o",this,i,this.options.collectionKey)}}else{if(i){j[i]=this.instance}}}j.bind("relational:add",this.handleAddition).bind("relational:remove",this.handleRemoval).bind("relational:reset",this.handleReset);return j},findRelated:function(i){if(this.keyContents){var j=[];if(this.keyContents instanceof h.Collection){j=this.keyContents.models}else{this.keyContents=d.isArray(this.keyContents)?this.keyContents:[this.keyContents];d.each(this.keyContents,function(l){var k=h.Relational.store.find(this.relatedModel,l);if(k&&d.isObject(l)){k.set(l,i)}else{if(!k){k=this.createModel(l)}}if(k&&!this.related.getByCid(k)&&!this.related.get(k)){j.push(k)}},this)}if(j.length){i=this.unsanitizeOptions(i);this.related.add(j,i)}}},onChange:function(l,i,k){k=this.sanitizeOptions(k);this.keyContents=i;d.each(this.getReverseRelations(),function(n){n.removeRelated(this.instance,k)},this);if(i instanceof h.Collection){this._prepareCollection(i);this.related=i}else{var m;if(this.related instanceof h.Collection){m=this.related;m.reset([],{silent:true})}else{m=this._prepareCollection()}this.setRelated(m);this.findRelated(k)}d.each(this.getReverseRelations(),function(n){n.addRelated(this.instance,k)},this);var j=this;h.Relational.eventQueue.add(function(){!k.silentChange&&j.instance.trigger("update:"+j.key,j.instance,j.related,k)})},tryAddRelated:function(j,i){i=this.sanitizeOptions(i);if(!this.related.getByCid(j)&&!this.related.get(j)){var k=d.any(this.keyContents,function(l){var m=h.Relational.store.resolveIdForItem(this.relatedModel,l);return m&&m===j.id},this);if(k){this.related.add(j,i)}}},handleAddition:function(k,l,j){if(!(k instanceof h.Model)){return}j=this.sanitizeOptions(j);d.each(this.getReverseRelations(k),function(m){m.addRelated(this.instance,j)},this);var i=this;h.Relational.eventQueue.add(function(){!j.silentChange&&i.instance.trigger("add:"+i.key,k,i.related,j)})},handleRemoval:function(k,l,j){if(!(k instanceof h.Model)){return}j=this.sanitizeOptions(j);d.each(this.getReverseRelations(k),function(m){m.removeRelated(this.instance,j)},this);var i=this;h.Relational.eventQueue.add(function(){!j.silentChange&&i.instance.trigger("remove:"+i.key,k,i.related,j)})},handleReset:function(k,j){j=this.sanitizeOptions(j);var i=this;h.Relational.eventQueue.add(function(){!j.silentChange&&i.instance.trigger("reset:"+i.key,i.related,j)})},addRelated:function(k,j){var i=this;j=this.unsanitizeOptions(j);k.queue(function(){if(i.related&&!i.related.getByCid(k)&&!i.related.get(k)){i.related.add(k,j)}})},removeRelated:function(j,i){i=this.unsanitizeOptions(i);if(this.related.getByCid(j)||this.related.get(j)){this.related.remove(j,i)}}});h.RelationalModel=h.Model.extend({relations:null,_relations:null,_isInitialized:false,_deferProcessing:false,_queue:null,constructor:function(j,k){var i=this;if(k&&k.collection){this._deferProcessing=true;var l=function(m){if(m===i){i._deferProcessing=false;i.processQueue();k.collection.unbind("relational:add",l)}};k.collection.bind("relational:add",l);d.defer(function(){l(i)})}this._queue=new h.BlockingQueue();this._queue.block();h.Relational.eventQueue.block();h.Model.prototype.constructor.apply(this,arguments);h.Relational.eventQueue.unblock()},trigger:function(j){if(j.length>5&&"change"===j.substr(0,6)){var i=this,k=arguments;h.Relational.eventQueue.add(function(){h.Model.prototype.trigger.apply(i,k)})}else{h.Model.prototype.trigger.apply(this,arguments)}return this},initializeRelations:function(){this.acquire();this._relations=[];d.each(this.relations,function(i){var j=!d.isString(i.type)?i.type:h[i.type]||h.Relational.store.getObjectByName(i.type);if(j&&j.prototype instanceof h.Relation.prototype.constructor){new j(this,i)}else{h.Relational.showWarnings&&typeof console!=="undefined"&&console.warn("Relation=%o; missing or invalid type!",i)}},this);this._isInitialized=true;this.release();this.processQueue()},updateRelations:function(i){if(this._isInitialized&&!this.isLocked()){d.each(this._relations,function(j){var k=this.attributes[j.key];if(j.related!==k){this.trigger("relational:change:"+j.key,this,k,i||{})}},this)}},queue:function(i){this._queue.add(i)},processQueue:function(){if(this._isInitialized&&!this._deferProcessing&&this._queue.isBlocked()){this._queue.unblock()}},getRelation:function(i){return d.detect(this._relations,function(j){if(j.key===i){return true}},this)},getRelations:function(){return this._relations},fetchRelated:function(n,p){p||(p={});var l,j=[],o=this.getRelation(n),q=o&&o.keyContents,m=q&&d.select(d.isArray(q)?q:[q],function(r){var s=h.Relational.store.resolveIdForItem(o.relatedModel,r);return s&&!h.Relational.store.find(o.relatedModel,s)},this);if(m&&m.length){var k=d.map(m,function(t){var s;if(typeof(t)==="object"){s=new o.relatedModel(t)}else{var r={};r[o.relatedModel.prototype.idAttribute]=t;s=new o.relatedModel(r)}return s},this);if(o.related instanceof h.Collection&&d.isFunction(o.related.url)){l=o.related.url(k)}if(l&&l!==o.related.url()){var i=d.defaults({error:function(){var r=arguments;d.each(k,function(s){s.trigger("destroy",s,s.collection,p);p.error&&p.error.apply(s,r)})},url:l},p,{add:true});j=[o.related.fetch(i)]}else{j=d.map(k,function(r){var s=d.defaults({error:function(){r.trigger("destroy",r,r.collection,p);p.error&&p.error.apply(r,arguments)}},p);return r.fetch(s)},this)}}return j},set:function(l,m,k){h.Relational.eventQueue.block();var j;if(d.isObject(l)||l==null){j=l;k=m}else{j={};j[l]=m}var i=h.Model.prototype.set.apply(this,arguments);if(!this._isInitialized&&!this.isLocked()){h.Relational.store.register(this);this.initializeRelations()}else{if(j&&this.idAttribute in j){h.Relational.store.update(this)}}if(j){this.updateRelations(k)}h.Relational.eventQueue.unblock();return i},unset:function(k,j){h.Relational.eventQueue.block();var i=h.Model.prototype.unset.apply(this,arguments);this.updateRelations(j);h.Relational.eventQueue.unblock();return i},clear:function(j){h.Relational.eventQueue.block();var i=h.Model.prototype.clear.apply(this,arguments);this.updateRelations(j);h.Relational.eventQueue.unblock();return i},change:function(k){var i=this,j=arguments;h.Relational.eventQueue.add(function(){h.Model.prototype.change.apply(i,j)})},clone:function(){var i=d.clone(this.attributes);if(!d.isUndefined(i[this.idAttribute])){i[this.idAttribute]=null}d.each(this.getRelations(),function(j){delete i[j.key]});return new this.constructor(i)},toJSON:function(){if(this.isLocked()){return this.id}this.acquire();var i=h.Model.prototype.toJSON.call(this);d.each(this._relations,function(j){var k=i[j.key];if(j.options.includeInJSON===true&&k&&d.isFunction(k.toJSON)){i[j.keyDestination]=k.toJSON()}else{if(d.isString(j.options.includeInJSON)){if(k instanceof h.Collection){i[j.keyDestination]=k.pluck(j.options.includeInJSON)}else{if(k instanceof h.Model){i[j.keyDestination]=k.get(j.options.includeInJSON)}}}else{delete i[j.key]}}if(j.keyDestination!==j.key){delete i[j.key]}},this);this.release();return i}});d.extend(h.RelationalModel.prototype,h.Semaphore);var f=h.Collection.prototype.__add=h.Collection.prototype.add;h.Collection.prototype.add=function(k,i){i||(i={});if(!d.isArray(k)){k=[k]}var j=[];d.each(k,function(m){if(!(m instanceof h.Model)){var l=h.Relational.store.find(this.model,m[this.model.prototype.idAttribute]);if(l){l.set(l.parse?l.parse(m):m,i);m=l}else{m=h.Collection.prototype._prepareModel.call(this,m,i)}}if(m instanceof h.Model&&!this.get(m)&&!this.getByCid(m)){j.push(m)}},this);if(j.length){f.call(this,j,i);d.each(j,function(l){this.trigger("relational:add",l,this,i)},this)}return this};var a=h.Collection.prototype.__remove=h.Collection.prototype.remove;h.Collection.prototype.remove=function(j,i){i||(i={});if(!d.isArray(j)){j=[j]}d.each(j,function(k){k=this.getByCid(k)||this.get(k);if(k instanceof h.Model){a.call(this,k,i);this.trigger("relational:remove",k,this,i)}},this);return this};var e=h.Collection.prototype.__reset=h.Collection.prototype.reset;h.Collection.prototype.reset=function(j,i){e.call(this,j,i);this.trigger("relational:reset",j,i);return this};var c=h.Collection.prototype.__trigger=h.Collection.prototype.trigger;h.Collection.prototype.trigger=function(j){if(j==="add"||j==="remove"||j==="reset"){var i=this,k=arguments;h.Relational.eventQueue.add(function(){c.apply(i,k)})}else{c.apply(this,arguments)}return this};h.RelationalModel.extend=function(j,k){var l=h.Model.extend.apply(this,arguments);var i=(j&&j.relations)||[];d.each(i,function(m){if(m.reverseRelation){m.model=l;var o=true;if(d.isString(m.relatedModel)){var n=h.Relational.store.getObjectByName(m.relatedModel);o=n&&(n.prototype instanceof h.RelationalModel.prototype.constructor)}var p=!d.isString(m.type)?m.type:h[m.type]||h.Relational.store.getObjectByName(m.type);if(o&&p&&p.prototype instanceof h.Relation.prototype.constructor){new p(null,m)}}});return l}})(); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/423f4f2910ac/ changeset: 423f4f2910ac user: jgoecks date: 2012-04-11 16:32:02 summary: Add Backbone-relational to base templates affected #: 2 files diff -r 0a957e499a3c9b7ba11f88d337e4878260d73d6d -r 423f4f2910ac90098e799d354a2936513242a21e templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -26,7 +26,7 @@ ##  - ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/handlebars.runtime", "backbone/ui" )} + ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/backbone-relational", "libs/handlebars.runtime", "backbone/ui" )} <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 0a957e499a3c9b7ba11f88d337e4878260d73d6d -r 423f4f2910ac90098e799d354a2936513242a21e templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -47,7 +47,7 @@  - ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/handlebars.runtime', 'backbone/ui' )} + ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/backbone-relational', 'libs/handlebars.runtime', 'backbone/ui' )} <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Basic functionality for accessing the API through session (if available) instead of via API key. Needs refactoring to combine _ensure_valid_session and transaction types.
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bf88ce609370/ changeset: bf88ce609370 user: dannon date: 2012-04-11 16:00:16 summary: Basic functionality for accessing the API through session (if available) instead of via API key. Needs refactoring to combine _ensure_valid_session and transaction types. affected #: 4 files diff -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad -r bf88ce609370a7829337dad758fafe388b3fd117 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -20,28 +20,27 @@ GET /api/histories GET /api/histories/deleted Displays a collection (list) of histories. - """ + """ rval = [] deleted = util.string_as_bool( deleted ) - try: - query = trans.sa_session.query( trans.app.model.History ).filter_by( user=trans.user, deleted=deleted ).order_by( - desc(trans.app.model.History.table.c.update_time)).all() + if trans.user: + query = trans.sa_session.query(trans.app.model.History ).filter_by( user=trans.user, deleted=deleted ).order_by( + desc(trans.app.model.History.table.c.update_time)).all() + for history in query: + item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) + rval.append( item ) + elif trans.galaxy_session.current_history: + #No user, this must be session authentication with an anonymous user. + history = trans.galaxy_session.current_history + item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) + rval.append(item) except Exception, e: rval = "Error in history API" log.error( rval + ": %s" % str(e) ) trans.response.status = 500 - - if not rval: - try: - for history in query: - item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) - item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - rval.append( item ) - except Exception, e: - rval = "Error in history API at constructing return list" - log.error( rval + ": %s" % str(e) ) - trans.response.status = 500 return rval @web.expose_api @@ -54,7 +53,7 @@ history_id = id params = util.Params( kwd ) deleted = util.string_as_bool( deleted ) - + def traverse( datasets ): rval = {} states = trans.app.model.Dataset.states @@ -65,15 +64,13 @@ if not item['deleted']: rval[item['state']] = rval[item['state']] + 1 return rval - try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: return str( e ) - try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) - num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) + num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) states = trans.app.model.Dataset.states state = states.ERROR if num_sets == 0: @@ -87,7 +84,7 @@ elif summary[states.QUEUED] > 0: state = states.QUEUED elif summary[states.OK] == num_sets: - state = states.OK + state = states.OK item['contents_url'] = url_for( 'history_contents', history_id=history_id ) item['state_details'] = summary item['state'] = state @@ -108,7 +105,7 @@ if payload.get( 'name', None ): hist_name = util.restore_text( payload['name'] ) new_history = trans.app.model.History( user=trans.user, name=hist_name ) - + trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) @@ -124,8 +121,8 @@ # a request body is optional here purge = False if kwd.get( 'payload', None ): - purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) - + purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) + try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) except Exception, e: diff -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad -r bf88ce609370a7829337dad758fafe388b3fd117 lib/galaxy/web/api/requests.py --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -1,19 +1,17 @@ """ API operations on a sample tracking system. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util +import logging +from galaxy import util, web from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * from galaxy.util.bunch import Bunch log = logging.getLogger( __name__ ) class RequestsAPIController( BaseAPIController ): - update_types = Bunch( REQUEST = 'request_state' ) - update_type_values = [v[1] for v in update_types.items()] + _update_types = Bunch( REQUEST = 'request_state' ) + _update_type_values = [v[1] for v in _update_types.items()] @web.expose_api def index( self, trans, **kwd ): """ @@ -77,7 +75,7 @@ return "Missing required 'update_type' parameter. Please consult the API documentation for help." else: update_type = payload.pop( 'update_type' ) - if update_type not in self.update_type_values: + if update_type not in self._update_type_values: trans.response.status = 400 return "Invalid value for 'update_type' parameter ( %s ) specified. Please consult the API documentation for help." % update_type try: diff -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad -r bf88ce609370a7829337dad758fafe388b3fd117 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -18,9 +18,9 @@ def index(self, trans, **kwd): """ GET /api/workflows - Displays a collection of workflows + + Displays a collection of workflows. """ - # List parameters of a specific workflow rval = [] for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter_by( user=trans.user, deleted=False).order_by( @@ -38,10 +38,12 @@ item['url'] = url_for('workflow', id=encoded_id) rval.append(item) return rval + @web.expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} + Displays information needed to run a workflow from the command line. """ workflow_id = id @@ -72,28 +74,29 @@ # p = step.get_required_parameters() item['inputs'] = inputs return item + @web.expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows + We're not creating workflows from the api. Just execute for now. + However, we will import them if installed_repository_file is specified """ if 'workflow_id' not in payload: # create new if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] - result = workflow_controller.import_workflow( trans=trans, + result = workflow_controller.import_workflow( trans=trans, cntrller='api', **payload) return result trans.response.status = 403 return "Either workflow_id or installed_repository_file must be specified" - if 'installed_repository_file' in payload: trans.response.status = 403 return "installed_repository_file may not be specified with workflow_id" - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get( trans.security.decode_id(payload['workflow_id'])) if stored_workflow.user != trans.user and not trans.user_is_admin(): @@ -215,3 +218,4 @@ trans.sa_session.add( workflow_invocation ) trans.sa_session.flush() return rval + diff -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad -r bf88ce609370a7829337dad758fafe388b3fd117 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -9,6 +9,7 @@ from Cheetah.Template import Template import base import pickle +from functools import wraps from galaxy import util from galaxy.exceptions import MessageException from galaxy.util.json import to_json_string, from_json_string @@ -62,6 +63,7 @@ return func def json( func ): + @wraps(func) def decorator( self, trans, *args, **kwargs ): trans.response.set_content_type( "text/javascript" ) return simplejson.dumps( func( self, trans, *args, **kwargs ) ) @@ -71,6 +73,7 @@ return decorator def json_pretty( func ): + @wraps(func) def decorator( self, trans, *args, **kwargs ): trans.response.set_content_type( "text/javascript" ) return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) @@ -81,37 +84,46 @@ def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): + @wraps(func) def decorator( self, trans, *args, **kwargs ): if trans.get_user(): return func( self, trans, *args, **kwargs ) else: return trans.show_error_message( 'You must be <a target="galaxy_main" href="%s">logged in</a> to %s.' - % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) + % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) return decorator return argcatcher - + def expose_api( func ): + @wraps(func) def decorator( self, trans, *args, **kwargs ): def error( environ, start_response ): start_response( error_status, [('Content-type', 'text/plain')] ) return error_message error_status = '403 Forbidden' - if 'key' not in kwargs: - error_message = 'No API key provided with request, please consult the API documentation.' - return error - try: - provided_key = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.key == kwargs['key'] ).one() - except NoResultFound: - error_message = 'Provided API key is not valid.' - return error - if provided_key.user.deleted: - error_message = 'User account is deactivated, please contact an administrator.' - return error - newest_key = provided_key.user.api_keys[0] - if newest_key.key != provided_key.key: - error_message = 'Provided API key has expired.' - return error + ## If there is a user, we've authenticated a session. + if not trans.user and isinstance(trans.galaxy_session, Bunch): + # If trans.user is already set, don't check for a key. + # This happens when we're authenticating using session instead of an API key. + # The Bunch clause is used to prevent the case where there's no user, but there is a real session. + # DBTODO: This needs to be fixed when merging transaction types. + if 'key' not in kwargs: + error_message = 'No API key provided with request, please consult the API documentation.' + return error + try: + provided_key = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.key == kwargs['key'] ).one() + except NoResultFound: + error_message = 'Provided API key is not valid.' + return error + if provided_key.user.deleted: + error_message = 'User account is deactivated, please contact an administrator.' + return error + newest_key = provided_key.user.api_keys[0] + if newest_key.key != provided_key.key: + error_message = 'Provided API key has expired.' + return error + trans.set_user( provided_key.user ) if trans.request.body: try: payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) @@ -121,7 +133,6 @@ error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' return error trans.response.set_content_type( "application/json" ) - trans.set_user( provided_key.user ) # Perform api_run_as processing, possibly changing identity if 'run_as' in kwargs: if not trans.user_can_do_run_as(): @@ -139,7 +150,6 @@ except: trans.response.status = 400 return "That user does not exist." - try: if trans.debug: return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) @@ -156,6 +166,7 @@ return decorator def require_admin( func ): + @wraps(func) def decorator( self, trans, *args, **kwargs ): if not trans.user_is_admin(): msg = "You must be an administrator to access this feature." @@ -202,10 +213,10 @@ return base.WebApplication.make_body_iterable( self, trans, body ) def transaction_chooser( self, environ, galaxy_app, session_cookie ): if 'is_api_request' in environ: - return GalaxyWebAPITransaction( environ, galaxy_app, self ) + return GalaxyWebAPITransaction( environ, galaxy_app, self, session_cookie ) else: return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) - + class GalaxyWebTransaction( base.DefaultWebTransaction ): """ Encapsulates web transaction specific state for the Galaxy application @@ -262,7 +273,7 @@ except: action.user = None try: - action.session_id = self.galaxy_session.id + action.session_id = self.galaxy_session.id except: action.session_id = None self.sa_session.add( action ) @@ -317,7 +328,7 @@ tstamp = time.localtime ( time.time() + 3600 * 24 * age ) self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) self.response.cookies[name]['version'] = version - def _ensure_valid_session( self, session_cookie ): + def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as trans.session (part of initialization) @@ -822,7 +833,7 @@ def add_select( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): self.inputs.append( SelectInput( name, label, value=value, options=options, error=error, help=help, use_label=use_label ) ) return self - + class FormInput( object ): """ Simple class describing a form input element @@ -837,15 +848,89 @@ self.use_label = use_label class GalaxyWebAPITransaction( GalaxyWebTransaction ): - def __init__( self, environ, app, webapp ): + """ + TODO: Unify this with WebUITransaction, since we allow session auth now. + Enable functionality of 'create' parameter in parent _ensure_valid_session + """ + def __init__( self, environ, app, webapp, session_cookie): GalaxyWebTransaction.__init__( self, environ, app, webapp ) self.__user = None - self._ensure_valid_session( None ) + self._ensure_valid_session( session_cookie ) def _ensure_valid_session( self, session_cookie ): - self.galaxy_session = Bunch() - self.galaxy_session.history = self.galaxy_session.current_history = Bunch() - self.galaxy_session.history.genome_build = None - self.galaxy_session.is_api = True + #Check to see if there is an existing session. Never create a new one. + # Try to load an existing session + secure_id = self.get_cookie( name=session_cookie ) + galaxy_session = None + prev_galaxy_session = None + user_for_new_session = None + invalidate_existing_session = False + # Track whether the session has changed so we can avoid calling flush + # in the most common case (session exists and is valid). + galaxy_session_requires_flush = False + if secure_id: + # Decode the cookie value to get the session_key + session_key = self.security.decode_guid( secure_id ) + try: + # Make sure we have a valid UTF-8 string + session_key = session_key.encode( 'utf8' ) + except UnicodeDecodeError: + # We'll end up creating a new galaxy_session + session_key = None + if session_key: + # Retrieve the galaxy_session id via the unique session_key + galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ + .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, + self.app.model.GalaxySession.table.c.is_valid==True ) ) \ + .first() + if galaxy_session: + # If remote user is in use it can invalidate the session, so we need to to check some things now. + if self.app.config.use_remote_user: + assert "HTTP_REMOTE_USER" in self.environ, \ + "use_remote_user is set but no HTTP_REMOTE_USER variable" + remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] + # An existing session, make sure correct association exists + if galaxy_session.user is None: + # No user, associate + galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) + galaxy_session_requires_flush = True + elif galaxy_session.user.email != remote_user_email: + # Session exists but is not associated with the correct remote user + log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", + remote_user_email, galaxy_session.user.email ) + galaxy_session = None + else: + if galaxy_session.user and galaxy_session.user.external: + # Remote user support is not enabled, but there is an existing + # session with an external user, invalidate + invalidate_existing_session = True + log.warning( "User '%s' is an external user with an existing session, invalidating session since external auth is disabled", + galaxy_session.user.email ) + galaxy_session = None + elif galaxy_session.user is not None and galaxy_session.user.deleted: + invalidate_existing_session = True + log.warning( "User '%s' is marked deleted, invalidating session" % galaxy_session.user.email ) + galaxy_session = None + # No relevant cookies, or couldn't find, or invalid, so create a new session + if galaxy_session: + self.galaxy_session = galaxy_session + self.user = galaxy_session.user + # Do we need to flush the session? + if galaxy_session_requires_flush: + self.sa_session.add( galaxy_session ) + # FIXME: If prev_session is a proper relation this would not + # be needed. + if prev_galaxy_session: + self.sa_session.add( prev_galaxy_session ) + self.sa_session.flush() + # If the old session was invalid, get a new history with our new session + if not galaxy_session: + #Failed to find a session. Set up fake stuff for API transaction + self.user = None + self.galaxy_session = Bunch() + self.galaxy_session.history = self.galaxy_session.current_history = Bunch() + self.galaxy_session.history.genome_build = None + self.galaxy_session.is_api = True + def get_user( self ): """Return the current user (the expose_api decorator ensures that it is set).""" return self.__user Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Cloud Launch - Password Field for AWS Secret instead of plain text input
by Bitbucket 11 Apr '12

11 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f12abbd2394/ changeset: 3f12abbd2394 user: dannon date: 2012-04-11 15:16:20 summary: Cloud Launch - Password Field for AWS Secret instead of plain text input affected #: 1 file diff -r 37c43980034e744d05647c3aad3631f5a1dd9c1c -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -71,7 +71,7 @@ </div><div class="form-row"><label for="id_secret">Secret Key</label> - <input type="text" size="120" name="secret" id="id_secret"/><br/> + <input type="password" size="120" name="secret" id="id_secret"/><br/></div><div class="form-row"><label for="id_instance_type">Instance Type</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Create object to store Galaxy paths for use in JavaScript.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/37c43980034e/ changeset: 37c43980034e user: jgoecks date: 2012-04-11 01:06:24 summary: Create object to store Galaxy paths for use in JavaScript. affected #: 10 files diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/backbone/ui.js --- a/static/scripts/backbone/ui.js +++ b/static/scripts/backbone/ui.js @@ -1,6 +1,16 @@ /** * Utility models and views for Galaxy objects. */ + +/** + * Necessary Galaxy paths. + */ +var GalaxyPaths = Backbone.Model.extend({ + defaults: { + root_path: "", + image_path: "" + } +}); /** * Clickable button represented as an icon. diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -217,7 +217,7 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + galaxy_paths.attributes.image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); $("#close_button").bind( "click", function() { hide_modal(); } ); } diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -188,7 +188,7 @@ .appendTo( "body" ) .append( $("<div class='buttons'></div>").append( - $("<img/>").attr("src", image_path + '/delete_icon.png').click( function() { + $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function() { $.each( terminal.connectors, function( _, x ) { x.destroy(); }); @@ -335,13 +335,13 @@ .css( { display: 'none' } ) .append( $("<div class='buttons'></div>").append( - $("<img/>").attr('src', image_path + '/fugue/asterisk-small-outline.png').click( function() { + $("<img/>").attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png').click( function() { if ($.inArray(output.name, node.workflow_outputs) != -1){ node.workflow_outputs.splice($.inArray(output.name, node.workflow_outputs), 1); - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ node.workflow_outputs.push(output.name); - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } workflow.has_changes = true; canvas_manager.draw_overview(); @@ -355,19 +355,19 @@ callout.show(); r.append(callout); if ($.inArray(output.name, node.workflow_outputs) === -1){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } r.hover( function(){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-yellow.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-yellow.png'); }, function(){ if ($.inArray(output.name, node.workflow_outputs) === -1){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } }); } @@ -793,18 +793,18 @@ f.append( title ); f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 ); var b = $("<div class='toolFormBody'></div>"); - var tmp = "<div><img height='16' align='middle' src='" +image_path+ "/loading_small_white_bg.gif'/> loading tool info...</div>"; + var tmp = "<div><img height='16' align='middle' src='" +galaxy_paths.attributes.image_path+ "/loading_small_white_bg.gif'/> loading tool info...</div>"; b.append( tmp ); node.form_html = tmp; f.append( b ); // Fix width to computed width // Now add floats var buttons = $("<div class='buttons' style='float: right;'></div>"); - buttons.append( $("<img/>").attr("src", image_path + '/delete_icon.png').click( function( e ) { + buttons.append( $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function( e ) { node.destroy(); } ).hover( - function() { $(this).attr( "src", image_path + "/delete_icon_dark.png" ); }, - function() { $(this).attr( "src", image_path + "/delete_icon.png" ); } + function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon_dark.png" ); }, + function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon.png" ); } ) ); // Place inside container f.appendTo( "#canvas-container" ); diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/packed/backbone/ui.js --- a/static/scripts/packed/backbone/ui.js +++ b/static/scripts/packed/backbone/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonView=Backbone.View.extend({tagName:"a",className:"icon-button menu-button",events:{click:"on_click"},render:function(){this.$el.attr("href","javascript:void(0)").attr("title",this.model.attributes.title).addClass(this.model.attributes.icon_class);return this},on_click:function(){this.model.attributes.on_click()}});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(c){var b=new IconButtonView({model:c});b.render();a.$el.append(b.$el)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file +var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. If visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.tiles_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae==="data"||ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={resize:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,ac,{content_div:ac.top_labeltrack,resize:false},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false);this.hide_contents()};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}this.show_contents();return new b(af,ad,ag,ae,ak)}this.hide_contents()}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=galaxy_paths.attributes.image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. If visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.tiles_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae==="data"||ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ag,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ag,ac);ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ah){});ad.postdraw_actions=ad.normal_postdraw_actions}}});var Y=function(ad,ac){var ae={resize:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,ac,{content_div:ac.top_labeltrack,resize:false},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false);this.hide_contents()};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}this.show_contents();return new b(af,ad,ag,ae,ak)}this.hide_contents()}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -207,8 +207,7 @@ var patterns = this.patterns, dummy_context = this.dummy_context, image = new Image(); - // FIXME: where does image_path come from? not in browser.mako... - image.src = image_path + path; + image.src = galaxy_paths.attributes.image_path + path; image.onload = function() { patterns[key] = dummy_context.createPattern( image, "repeat" ); } diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -27,6 +27,13 @@ ## <script type='text/javascript' src="/static/scripts/IE7.js"></script> ## <![endif]--> ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/handlebars.runtime", "backbone/ui" )} + <script type="text/javascript"> + // Set up needed paths. + var galaxy_paths = new GalaxyPaths({ + root_path: '${h.url_for( "/" )}', + image_path: '${h.url_for( "/static/images" )}' + }); + </script></%def> ## Additional metas can be defined by templates inheriting from this one. diff -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 -r 37c43980034e744d05647c3aad3631f5a1dd9c1c templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -47,10 +47,14 @@  + ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/handlebars.runtime', 'backbone/ui' )} <script type="text/javascript"> - var image_path = '${h.url_for("/static/images")}'; + // Set up needed paths. + var galaxy_paths = new GalaxyPaths({ + root_path: '${h.url_for( "/" )}', + image_path: '${h.url_for( "/static/images" )}' + }); </script> - ${h.js( 'jquery', 'libs/underscore', 'libs/backbone', 'libs/handlebars.runtime', 'backbone/ui' )} </%def> ## Default late-load javascripts Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: New config option, and change in default behavior regarding dataset path display in View Details. Administrators can now *always* see the full path, and if the expose_dataset_path option is True, so can regular users.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dae7eefe2f71/ changeset: dae7eefe2f71 user: dannon date: 2012-04-10 22:46:49 summary: New config option, and change in default behavior regarding dataset path display in View Details. Administrators can now *always* see the full path, and if the expose_dataset_path option is True, so can regular users. affected #: 3 files diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -106,6 +106,7 @@ self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) self.start_job_runners = kwargs.get( 'start_job_runners', None ) + self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) ) # External Service types used in sample tracking self.external_service_type_config_file = resolve_path( kwargs.get( 'external_service_type_config_file', 'external_service_types_conf.xml' ), self.root ) self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root ) diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -52,6 +52,9 @@ <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr><tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr> + %if trans.user_is_admin() or trans.app.config.expose_dataset_path: + <tr><td>Full Path:</td><td>${hda.file_name}</td></tr> + %endif </table><br /><table class="tabletip"> diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -678,6 +678,10 @@ #pbs_stage_path = #pbs_dataset_server = +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + # ---- Per-Tool Job Management ---------------------------------------------- # Per-tool job handler and runner overrides. Parameters can be included to define multiple Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add argument names to parameter help for GATK tools' options.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d59674927a52/ changeset: d59674927a52 user: dan date: 2012-04-10 22:22:45 summary: Add argument names to parameter help for GATK tools' options. affected #: 16 files diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -24,7 +24,7 @@ ' </command><inputs> - <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" /> + <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /><conditional name="analysis_param_type"><param name="analysis_param_type_selector" type="select" label="Basic or Advanced options"><option value="basic" selected="True">Basic</option> @@ -34,11 +34,11 @@ </when><when value="advanced"> - <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number."/> - <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups."/> - <param name="max_quality_score" type="integer" value="50" label="Max quality score"/> - <param name="max_histogram_value" type="integer" value="0" label="Max histogram value"/> - <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality"/> + <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number." help="-ignoreQ,--ignoreQ &lt;ignoreQ&gt; "/> + <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups." help="-numRG,--numRG &lt;numRG&gt;"/> + <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &lt;max_quality_score&gt;"/> + <param name="max_histogram_value" type="integer" value="0" label="Max histogram value" help="-maxHist,--max_histogram_value &lt;max_histogram_value&gt;"/> + <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality" help="--do_indel_quality"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -144,25 +144,28 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" > + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> - <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" /> - <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" > + <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" /> + <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &lt;covariate&gt;" ><option value="ReadGroupCovariate" /><option value="QualityScoreCovariate" /> @@ -178,7 +181,7 @@ <option value="TileCovariate" /></param> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites &lt;knownSites&gt;"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -427,7 +430,7 @@ </when><when value="advanced"><conditional name="default_read_group_type"> - <param name="default_read_group_type_selector" type="select" label="Set default Read Group"> + <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group"><option value="default" selected="True">Don't Set</option><option value="set">Set</option></param> @@ -438,14 +441,14 @@ <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/></when></conditional> - <param name="default_platform" type="select" label="Set default Platform"> + <param name="default_platform" type="select" label="Set default Platform" help="--default_platform"><option value="default" selected="True">Don't Set</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param><conditional name="force_read_group_type"> - <param name="force_read_group_type_selector" type="select" label="Force Read Group"> + <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group"><option value="default" selected="True">Don't Force</option><option value="set">Force</option></param> @@ -456,13 +459,13 @@ <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/></when></conditional> - <param name="force_platform" type="select" label="Force Platform"> + <param name="force_platform" type="select" label="Force Platform" help="--force_platform"><option value="default" selected="True">Don't Force</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param> - <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/> + <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/><conditional name="solid_options_type"><param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"><option value="default" selected="True">Don't Set</option> @@ -472,14 +475,14 @@ </when><when value="set"> - <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted"> + <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &lt;solid_recal_mode&gt;"><option value="default" selected="True">Don't set</option><option value="DO_NOTHING">DO_NOTHING</option><option value="SET_Q_ZERO">SET_Q_ZERO</option><option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option><option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option></param> - <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls"> + <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &lt;solid_nocall_strategy&gt;"><option value="default" selected="True">Don't set</option><option value="THROW_EXCEPTION">THROW_EXCEPTION</option><option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> @@ -487,8 +490,8 @@ </param></when></conditional> - <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/> - <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" /> + <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/> + <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &lt;homopolymer_nback&gt;" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -190,13 +190,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -204,27 +204,26 @@ </param></when><when value="history"> - <repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> + <param name="input_bam" type="data" format="bam" label="BAM file" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" /> + <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" /> - <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes"> + <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;"><option value="sample" selected="True">sample</option><option value="readgroup">readgroup</option><option value="library">library</option></param> - <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold"> + <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;"><param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" /></repeat> - <param name="output_format" type="select" label="Output format" > + <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" ><option value="csv">csv</option><option value="table">table</option><option value="rtable" selected="True">rtable</option> @@ -450,21 +449,21 @@ </when><when value="advanced"> - <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" /> - <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" /> - <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" /> - <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" /> - <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." /> - <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" /> - <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" /> - <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" /> - <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" /> - <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" /> - <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." /> - <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" /> - <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" /> - <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" /> - <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" /> + <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> + <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> + <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" /> + <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" /> + <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" /> + <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &lt;minMappingQuality&gt;" /> + <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" /> + <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" /> + <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" /> + <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" /> + <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" /> + <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" /> + <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" /> + <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" /> + <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -122,29 +122,28 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> - <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options> - <filter type="data_meta" key="dbkey" ref="input_bam" /> + <filter type="data_meta" key="dbkey" ref="input_bam" /></options></param></when></conditional> - <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" help="-targetIntervals,--targetIntervals &lt;targetIntervals&gt;" /> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--knownAlleles &lt;knownAlleles&gt;"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -167,8 +166,8 @@ </when></conditional></repeat> - <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" /> - <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs"/> + <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &lt;LODThresholdForCleaning&gt;" /> + <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -391,19 +390,19 @@ </when><when value="advanced"> - <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" /> - <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/> - <param name="consensus_determination_model" type="select" label="Consensus Determination Model"> + <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &lt;entropyThreshold&gt;" /> + <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> + <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &lt;consensusDeterminationModel&gt;"><option value="KNOWNS_ONLY">KNOWNS_ONLY</option><option value="USE_READS" selected="True">USE_READS</option><option value="USE_SW">USE_SW</option></param> - <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" /> - <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" /> - <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" /> - <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" /> - <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" /> - <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam"/> + <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &lt;maxIsizeForMovement&gt;" /> + <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &lt;maxPositionalMoveAllowed&gt;" /> + <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &lt;maxConsensuses&gt;" /> + <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &lt;maxReadsForConsensuses&gt;" /> + <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &lt;maxReadsForRealignment&gt;" /> + <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -106,13 +106,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -120,21 +120,21 @@ </param></when><when value="history"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"><param name="input_bam" type="data" format="bam" label="BAM file" ></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" /> - <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" /> - <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" /> - <repeat name="sample_file_repeat" title="File containing a list of samples to include"> + <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &lt;number&gt;" /> + <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" /> + <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &lt;readGroup&gt;" /> + <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&gt;"><param name="input_sample_file" type="data" format="text" label="Sample file" /></repeat> - <repeat name="sample_name_repeat" title="Sample name to be included in the analysis"> + <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &lt;sample_name&gt;"><param name="sample_name" type="text" label="Sample name" /></repeat> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -110,11 +110,11 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> @@ -122,17 +122,16 @@ </param></when><when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> - <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options> - <filter type="data_meta" key="dbkey" ref="input_bam" /> + <filter type="data_meta" key="dbkey" ref="input_bam" /></options></param></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &lt;known&gt;"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -376,10 +375,10 @@ </when><when value="advanced"> - <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" /> - <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1"/> - <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" /> - <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" /> + <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &lt;windowSize&gt;" /> + <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction &lt;mismatchFraction&gt;)"/> + <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &lt;minReadsAtLocus&gt;" /> + <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &lt;maxIntervalSize&gt;" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -120,28 +120,31 @@ #end if </command><inputs> - <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" /> + <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /><conditional name="reference_source"><param name="reference_source_selector" type="select" label="Choose the source for the reference list"><option value="cached">Locally cached</option><option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" > + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> @@ -367,7 +370,7 @@ </when><when value="advanced"><conditional name="default_read_group_type"> - <param name="default_read_group_type_selector" type="select" label="Set default Read Group"> + <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group"><option value="default" selected="True">Don't Set</option><option value="set">Set</option></param> @@ -378,14 +381,14 @@ <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/></when></conditional> - <param name="default_platform" type="select" label="Set default Platform"> + <param name="default_platform" type="select" label="Set default Platform" help="--default_platform"><option value="default" selected="True">Don't Set</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param><conditional name="force_read_group_type"> - <param name="force_read_group_type_selector" type="select" label="Force Read Group"> + <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group"><option value="default" selected="True">Don't Force</option><option value="set">Force</option></param> @@ -396,13 +399,13 @@ <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/></when></conditional> - <param name="force_platform" type="select" label="Force Platform"> + <param name="force_platform" type="select" label="Force Platform" help="--force_platform"><option value="default" selected="True">Don't Force</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param> - <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/> + <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/><conditional name="solid_options_type"><param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"><option value="default" selected="True">Don't Set</option> @@ -412,14 +415,14 @@ </when><when value="set"> - <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted"> + <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &lt;solid_recal_mode&gt;"><option value="default" selected="True">Don't set</option><option value="DO_NOTHING">DO_NOTHING</option><option value="SET_Q_ZERO">SET_Q_ZERO</option><option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option><option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option></param> - <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls"> + <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &lt;solid_nocall_strategy&gt;"><option value="default" selected="True">Don't set</option><option value="THROW_EXCEPTION">THROW_EXCEPTION</option><option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> @@ -427,13 +430,13 @@ </param></when></conditional> - <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/> - <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/> - <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" /> - <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated"/> - <param name="smoothing" type="integer" value="1" label="smoothing"/> - <param name="max_quality_score" type="integer" value="50" label="Max quality score"/> - <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag"/> + <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> + <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/> + <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &lt;homopolymer_nback&gt;" /> + <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &lt;preserve_qscores_less_than&gt;"/> + <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &lt;smoothing&gt;"/> + <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &lt;max_quality_score&gt;"/> + <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -155,13 +155,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -169,15 +169,15 @@ </param></when><when value="history"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"><param name="input_bam" type="data" format="bam" label="BAM file" ></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp &lt;dbsnp&gt;"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -201,14 +201,14 @@ </conditional></repeat> - <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ"> + <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &lt;genotype_likelihoods_model&gt;"><option value="BOTH" selected="True">BOTH</option><option value="SNP">SNP</option><option value="INDEL">INDEL</option></param> - <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" /> - <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" /> + <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &lt;standard_min_confidence_threshold_for_calling&gt;" /> + <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &lt;standard_min_confidence_threshold_for_emitting&gt;" /><conditional name="gatk_param_type"> @@ -431,14 +431,14 @@ </when><when value="advanced"> - <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ"> + <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &lt;p_nonref_model&gt;"><option value="EXACT" selected="True">EXACT</option><option value="GRID_SEARCH">GRID_SEARCH</option></param> - <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" /> - <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" /> + <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &lt;heterozygosity&gt;" /> + <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &lt;pcr_error_rate&gt;" /><conditional name="genotyping_mode_type"> - <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping"> + <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &lt;genotyping_mode&gt;"><option value="DISCOVERY" selected="True">DISCOVERY</option><option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option></param> @@ -446,32 +446,32 @@ </when><when value="GENOTYPE_GIVEN_ALLELES"> - <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" /> + <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" /></when></conditional> - <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?"> + <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &lt;output_mode&gt;"><option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option><option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option><option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option></param> - <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" /> - <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" /> - <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1" /> - <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" /> - <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" /> - <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/> - <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" /> - <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" /> - <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /> - <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /> - <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> + <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" /> + <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" /> + <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" /> + <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> + <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" /> + <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/> + <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" /> + <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" /> + <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> + <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options></param> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> - <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option> @@ -497,14 +497,14 @@ </param> - <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" ><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options></param> - <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" /> + <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -150,13 +150,13 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." > + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;"/> + <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &lt;input_file&gt;)" ><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -164,11 +164,11 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" > + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;"/> + <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &lt;input_file&gt;)" ></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional><conditional name="annotations_type"> @@ -180,7 +180,7 @@ </when><when value="choose"> - <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > + <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &lt;annotation&gt;" ><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/> @@ -190,17 +190,17 @@ </when></conditional> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> - <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;"><param name="comp_input_rod" type="data" format="vcf" label="ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/></repeat><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -213,13 +213,13 @@ </when></conditional> - <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data"> + <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &lt;resource&gt;"><param name="resource_input_rod" type="data" format="vcf" label="ROD file" /><param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/></repeat><conditional name="snpEff_rod_bind_type"> - <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> + <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &lt;snpEffFile&gt;"><option value="set_snpEff">Set snpEff</option><option value="exclude_snpEff" selected="True">Don't set snpEff</option></param> @@ -232,7 +232,7 @@ </when></conditional> - <repeat name="expressions" title="Expression"> + <repeat name="expressions" title="Expression" help="-E,--expression &lt;expression&gt;"><param name="expression" type="text" value="" label="Expression"/></repeat> @@ -447,16 +447,16 @@ </when></conditional> - <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls"> + <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &lt;group&gt;"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option></param> - <param name="family_string" type="text" value="" label="Family String"/> - <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/> - <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > + <param name="family_string" type="text" value="" label="Family String" help="--family_string"/> + <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &lt;MendelViolationGenotypeQualityThreshold&gt;"/> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" ><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -104,12 +104,12 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> - <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/></repeat> - <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /> - <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> + <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -117,12 +117,12 @@ </param></when><when value="history"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"><param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /></repeat> - <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /> - <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> + <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> @@ -337,12 +337,12 @@ </when></conditional> - <param name="mode" type="select" label="Recalibration mode"> + <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"><option value="SNP" selected="True">SNP</option><option value="INDEL">INDEL</option><option value="BOTH">BOTH</option></param> - <repeat name="ignore_filters" title="Ignore Filter"> + <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"><conditional name="ignore_filter_type"><param name="ignore_filter_type_selector" type="select" label="Filter Type"><option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> @@ -352,9 +352,11 @@ <when value="custom"><param name="filter_name" type="text" value="" label="Filter name"/></when> + <when value="HARD_TO_VALIDATE" /> + <when value="LowQual" /></conditional></repeat> - <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/> + <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/></inputs><outputs><data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" /> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -115,13 +115,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -129,17 +129,17 @@ </param></when><when value="history"> - <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" > + <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &lt;genotypemergeoption&gt;" ><option value="UNIQUIFY" /><option value="PRIORITIZE" selected="true"/><option value="UNSORTED" /> @@ -367,18 +367,18 @@ </when><when value="advanced"> - <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields? " > + <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &lt;filteredrecordsmergetype&gt;" ><option value="KEEP_IF_ANY_UNFILTERED" selected="true"/><option value="KEEP_IF_ALL_UNFILTERED" /></param> - <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" /> - <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" /> - <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" /> + <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" /> + <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" /> + <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" /> - <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from."/> - <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." /> - <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files."/> + <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &lt;setKey&gt;"/> + <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" /> + <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &lt;minimumN&gt;"/></when></conditional> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -163,10 +163,10 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"><param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -174,21 +174,21 @@ </param></when><when value="history"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"><param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;"><param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> - <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" /> + <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;"/></repeat><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -198,7 +198,7 @@ <when value="set_dbsnp"><param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /><param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> - <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" /> + <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;" /></when></conditional> @@ -424,7 +424,7 @@ </when><when value="advanced"><repeat name="stratifications" title="Stratification"> - <param name="select_exps" value="" type="text" label="Stratification Expression"> + <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &lt;select_exps&gt;"><sanitizer><valid initial="string.printable"><remove value="'"/> @@ -432,14 +432,14 @@ <mapping initial="none"/></sanitizer></param> - <param name="select_name" value="" type="text" label="Name"/> + <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &lt;select_names&gt;"/></repeat> - <repeat name="samples" title="Sample"> + <repeat name="samples" title="Sample" help="-sn,--sample &lt;sample&gt;"><param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/></repeat> - <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" > + <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &lt;stratificationModule&gt;" ><option value="AlleleFrequency" /><option value="AlleleCount" /> @@ -454,13 +454,13 @@ <option value="Sample" /><option value="IntervalStratification" /></param> - <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" /> + <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" /> - <repeat name="only_variants_of_type" title="only Variants Of Type"> + <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"><param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/></repeat> - <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" > + <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &lt;evalModule&gt;" ><option value="ACTransitionTable" /><option value="AlleleFrequencyComparison" /> @@ -479,15 +479,15 @@ <option value="TiTvVariantEvaluator" /><option value="VariantQualityScore" /></param> - <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" /> + <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" /> - <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file " value="0"/> - <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0"/> - <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined"/> - <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50"/> - <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" /> - <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" /> - <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" /> + <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &lt;numSamples&gt;"/> + <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &lt;minPhaseQuality&gt;"/> + <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/> + <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;"/> + <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &lt;ancestralAlignments&gt;" /> + <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &lt;knownCNVs&gt;" /> + <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &lt;stratIntervals&gt;" /></when></conditional> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -109,8 +109,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -118,14 +118,14 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional><repeat name="variant_filters" title="Variant Filters"> - <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions"> + <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)"><sanitizer><valid initial="string.printable"><remove value="'"/> @@ -133,8 +133,8 @@ <mapping initial="none"/></sanitizer></param> - <param name="filter_name" value="custom_filter" type="text" label="Filter name"/> - <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" /> + <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> + <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" /></repeat> @@ -148,9 +148,9 @@ </when><when value="set_mask"> - <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" /> - <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/> - <param name="mask_extension" type="integer" value="0" label="Mask Extension"/> + <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> + <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> + <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/></when></conditional> @@ -375,12 +375,12 @@ </when><when value="cluster_snp"> - <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster "/> - <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs"/> + <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/> + <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/></when></conditional> - <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" /> + <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /></inputs><outputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -34,9 +34,9 @@ #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": - -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #else: - -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #end if #end for @@ -156,10 +156,10 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"><param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"></options> @@ -167,14 +167,14 @@ </param></when><when value="history"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"><param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -185,6 +185,7 @@ <option value="omni">OMNI</option><option value="mask">Mask</option><option value="custom">Custom</option> + <option value="comp">Comp</option></param><when value="variant"><param name="input_rod" type="data" format="vcf" label="Variant ROD file" /> @@ -225,6 +226,25 @@ </when></conditional></when> + <when value="mask"> + <param name="input_rod" type="data" format="vcf" label="ROD file" /> + <conditional name="rod_training_type"> + <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> + <option value="is_training_truth_known">Set training/truth/known sites</option> + <option value="not_training_truth_known" selected="True">Don't Set options</option> + </param> + <when value="not_training_truth_known"> +  + </when> + <when value="is_training_truth_known"> + <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> + <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> + <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> + <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> + <param name="prior" type="float" label="prior probability of being true" value="12.0"/> + </when> + </conditional> + </when><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"> @@ -343,7 +363,7 @@ </conditional></repeat> - <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations"> + <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/> @@ -351,11 +371,11 @@ </options></param> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> - <param name="mode" type="select" label="Recalibration mode"> + <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"><option value="SNP" selected="True">SNP</option><option value="INDEL">INDEL</option><option value="BOTH">BOTH</option> @@ -581,29 +601,29 @@ </when><when value="advanced"> - <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10"/> - <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100"/> - <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30"/> - <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0"/> - <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0"/> - <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0"/> - <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/> - <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/> + <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &lt;maxGaussians&gt;"/> + <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &lt;maxIterations&gt;"/> + <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans &lt;numKMeans&gt;"/> + <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0" help="-std,--stdThreshold &lt;stdThreshold&gt;"/> + <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold &lt;qualThreshold&gt;"/> + <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/> + <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/> + <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &lt;priorCounts&gt;"/><conditional name="bad_variant_selector"><param name="bad_variant_selector_type" type="select" label="How to specify bad variants"><option value="percent" selected="True">Percent</option><option value="min_num">Number</option></param><when value="percent"> - <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/> + <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants &lt;percentBadVariants&gt;"/></when><when value="min_num"> - <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/> + <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants &lt;minNumBadVariants&gt;"/></when></conditional> - <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15"/> - <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0"/> - <repeat name="ignore_filters" title="Ignore Filter"> + <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv &lt;target_titv&gt;"/> + <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche &lt;TStranche&gt;"/> + <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"><conditional name="ignore_filter_type"><param name="ignore_filter_type_selector" type="select" label="Filter Type"><option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> @@ -613,9 +633,11 @@ <when value="custom"><param name="filter_name" type="text" value="" label="Filter name"/></when> + <when value="HARD_TO_VALIDATE" /> + <when value="LowQual" /></conditional></repeat> - <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/> + <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -162,8 +162,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -171,12 +171,12 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional> - <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data"> + <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &lt;select_expressions&gt;"><param name="select_expressions" type="text" label="JEXL expression"><sanitizer><valid initial="string.printable"> @@ -187,18 +187,18 @@ </param></repeat> - <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True"/> - <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True"/> + <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &lt;concordance&gt;"/> + <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &lt;discordance&gt;"/> - <repeat name="sample_name_repeat" title="Include Samples by name"> + <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &lt;sample_name&gt;"><param name="sample_name" type="text" label="Include genotypes from this sample"/></repeat> - <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name"> + <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &lt;exclude_sample_name&gt;"><param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/></repeat> - <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" /> + <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" /><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -422,31 +422,31 @@ </when><when value="advanced"> - <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file"> + <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;"><param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/></repeat> - <repeat name="sample_file_repeat" title="Samples by file"> + <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;"><param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /></repeat> - <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True"/> + <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> - <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" /> + <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" /> - <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" /> + <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> - <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" /> + <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;" /> - <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" /> + <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &lt;remove_fraction_genotypes&gt;" /> - <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity"> + <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &lt;restrictAllelesTo&gt;"><option value="ALL" selected="True">ALL</option><option value="MULTIALLELIC">MULTIALLELIC</option><option value="BIALLELIC">BIALLELIC</option></param> - <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided"> + <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &lt;sample_expressions&gt;"><param name="sample_expressions" type="text" label="Regular expression"><sanitizer><valid initial="string.printable"> @@ -467,16 +467,16 @@ </when><when value="select_random_fraction"> - <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1"/> + <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &lt;select_random_fraction&gt;"/></when><when value="select_random_number"> - <param name="select_random_number" type="integer" value="0" label="Count" /> + <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &lt;select_random_number&gt;" /></when></conditional> - <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" /> + <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" /> - <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes"> + <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &lt;selectTypeToInclude&gt;"><option value="INDEL">INDEL</option><option value="SNP">SNP</option><option value="MIXED">MIXED</option> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -95,8 +95,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -104,13 +104,13 @@ </param></when><when value="history"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /></when></conditional><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -123,8 +123,8 @@ </when></conditional> - <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen. "/> - <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed. "/> + <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/> + <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix inconsequential warning about when tag when loading FreeBayes.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/25edd75ca72f/ changeset: 25edd75ca72f user: dan date: 2012-04-10 22:08:15 summary: Fix inconsequential warning about when tag when loading FreeBayes. affected #: 1 file diff -r b148fcea038fa00867a3c0e260e8d255a0a08ecb -r 25edd75ca72fd9c276476203e05c093e949b37eb tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -241,7 +241,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -257,7 +257,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -289,7 +289,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -311,7 +311,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -352,7 +352,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -368,7 +368,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> @@ -384,7 +384,7 @@ <option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param> - <when value="do_no_set"> + <when value="do_not_set"></when><when value="set"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix inconsequential warning about when tag when loading samtools mpileup.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b148fcea038f/ changeset: b148fcea038f user: dan date: 2012-04-10 22:07:19 summary: Fix inconsequential warning about when tag when loading samtools mpileup. affected #: 1 file diff -r 09ce2f09585514d6ce60ef3cd3dc56d9edd526e4 -r b148fcea038fa00867a3c0e260e8d255a0a08ecb tools/samtools/samtools_mpileup.xml --- a/tools/samtools/samtools_mpileup.xml +++ b/tools/samtools/samtools_mpileup.xml @@ -97,7 +97,7 @@ <when value="perform_indel_calling"><param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" /></when> - <when value="do_no_perform_indel_calling" /> + <when value="do_not_perform_indel_calling" /></conditional><param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" /><repeat name="platform_list_repeat" title="Platform for INDEL candidates"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Whitespace cleanup.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/09ce2f095855/ changeset: 09ce2f095855 user: dannon date: 2012-04-10 20:41:26 summary: Whitespace cleanup. affected #: 1 file diff -r b9c0762a09db90952ebd51ce123927f097cd68ff -r 09ce2f09585514d6ce60ef3cd3dc56d9edd526e4 lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -21,12 +21,11 @@ """ GET /api/histories/{encoded_history_id}/contents Displays a collection (list) of history contents - """ + """ try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) except Exception, e: return str( e ) - rval = [] try: for dataset in history.datasets: @@ -67,7 +66,7 @@ item = self.encode_all_ids( trans, item ) except Exception, e: item = "Error in history API at listing dataset" - log.error( item + ": %s" % str(e) ) + log.error( item + ": %s" % str(e) ) trans.response.status = 500 return item Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Fix history_contents API adding the HDA to the history twice (resulting in skipped hids)
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b9c0762a09db/ changeset: b9c0762a09db user: dannon date: 2012-04-10 20:32:13 summary: Fix history_contents API adding the HDA to the history twice (resulting in skipped hids) affected #: 1 file diff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 -r b9c0762a09db90952ebd51ce123927f097cd68ff lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -95,7 +95,6 @@ except Exception, e: return str( e ) hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) - history.add_dataset( hda ) trans.sa_session.flush() return hda.get_api_value() else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Update argument names to parameter help for GATK Advanced options.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/99b2fe57e167/ changeset: 99b2fe57e167 user: dan date: 2012-04-10 17:46:46 summary: Update argument names to parameter help for GATK Advanced options. affected #: 15 files diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -215,17 +215,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -327,20 +327,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -355,10 +355,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -369,34 +369,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,17 +239,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -351,20 +351,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -379,10 +379,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -393,34 +393,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -179,17 +179,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -291,20 +291,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -319,10 +319,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -333,34 +333,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,17 +147,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -259,20 +259,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -287,10 +287,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -301,34 +301,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -165,17 +165,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -277,20 +277,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -305,10 +305,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -319,34 +319,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,17 +154,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -266,20 +266,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -294,10 +294,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -308,34 +308,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -220,17 +220,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -332,20 +332,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -360,10 +360,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -374,34 +374,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,17 +245,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -357,20 +357,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -385,10 +385,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -399,34 +399,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,17 +135,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -247,20 +247,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -275,10 +275,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -289,34 +289,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,17 +155,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -267,20 +267,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -295,10 +295,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -309,34 +309,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,17 +211,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -323,20 +323,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -351,10 +351,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -365,34 +365,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,17 +164,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -276,20 +276,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -304,10 +304,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -318,34 +318,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -370,17 +370,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -482,20 +482,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -510,10 +510,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -524,34 +524,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,17 +209,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -321,20 +321,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -349,10 +349,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -363,34 +363,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,17 +135,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -247,20 +247,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -275,10 +275,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -289,34 +289,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 10 Apr '12

10 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e780ec798c93/ changeset: e780ec798c93 user: jgoecks date: 2012-04-10 17:19:47 summary: Backbone UI enhancements: create collection of tools in tool panel and use to get model when a tool link is clicked. affected #: 1 file diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r e780ec798c9373e475d2bc698c0d991fc7baa166 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -45,6 +45,13 @@ }); /** + * Wrap collection of tools for fast access/manipulation. + */ +var ToolCollection = Backbone.Collection.extend({ + model: Tool +}); + +/** * Label or section header in tool panel. */ var ToolPanelLabel = BaseModel.extend({}); @@ -149,6 +156,8 @@ */ var ToolPanel = Backbone.Collection.extend({ url: "/tools", + tools: new ToolCollection(), + parse: function(response) { // Recursive function to parse tool panel elements. var parse_elt = function(elt_dict) { @@ -173,6 +182,27 @@ initialize: function(options) { this.tool_search = options.tool_search; this.tool_search.on("change:results", this.apply_search_results, this); + this.on("reset", this.populate_tools, this); + }, + + /** + * Populate tool collection from panel elements. + */ + populate_tools: function() { + var self = this; + self.tools = new ToolCollection(); + this.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + _.each(panel_elt.attributes.elems, function (section_elt) { + if (section_elt instanceof Tool) { + self.tools.push(section_elt); + } + }); + } + else if (panel_elt instanceof Tool) { + self.tools.push(panel_elt); + } + }); }, clear_search_results: function() { @@ -358,34 +388,51 @@ */ initialize: function(options) { this.collection.tool_search.on("change:results", this.handle_search_results, this); + + this.tool_link_click_fn = null; + if (options && 'tool_link_click_fn' in options) { + this.tool_link_click_fn = options.tool_link_click_fn; + } }, render: function() { - var this_el = this.$el; + var self = this; // Render search. var search_view = new ToolSearchView( {model: this.collection.tool_search} ); search_view.render(); - this_el.append(search_view.$el); + self.$el.append(search_view.$el); // Render panel. this.collection.each(function(panel_elt) { if (panel_elt instanceof ToolPanelSection) { var section_title_view = new ToolPanelSectionView({model: panel_elt}); section_title_view.render(); - this_el.append(section_title_view.$el); + self.$el.append(section_title_view.$el); } else if (panel_elt instanceof Tool) { var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); tool_view.render(); - this_el.append(tool_view.$el); + self.$el.append(tool_view.$el); } else if (panel_elt instanceof ToolPanelLabel) { var label_view = new ToolPanelLabelView({model: panel_elt}); label_view.render(); - this_el.append(label_view.$el); + self.$el.append(label_view.$el); } }); + + // Setup tool link click handling. + if (self.tool_link_click_fn) { + self.$el.find("a.tool-link").click(function() { + // Tool id is always the first class. + var tool_id = $(this).attr('class').split(/\s+/)[0]; + + self.tool_link_click_fn(self.collection.tools.get(tool_id)); + return false; + }); + } + return this; }, https://bitbucket.org/galaxy/galaxy-central/changeset/bc94cf3ea6d0/ changeset: bc94cf3ea6d0 user: jgoecks date: 2012-04-10 17:21:37 summary: Merge affected #: 15 files diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -180,13 +180,13 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="mask">Mask</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /></when> @@ -215,204 +215,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,204 +239,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -996,25 +996,25 @@ **Settings**:: - calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. - ignoreDeletionSites boolean false Ignore sites consisting only of deletions - includeDeletions boolean false Include information on deletions - maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). - maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). - minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. - minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. - nBins int 499 Number of bins to use for granular binning - omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup - omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup - omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup - omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. - outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table - partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. - printBaseCounts boolean false Will add base counts to per-locus output. - printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. - start int 1 Starting (left endpoint) for granular binning - stop int 500 Ending (right endpoint) for granular binning - summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. + calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. + ignoreDeletionSites boolean false Ignore sites consisting only of deletions + includeDeletions boolean false Include information on deletions + maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). + maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). + minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. + minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. + nBins int 499 Number of bins to use for granular binning + omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup + omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup + omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup + omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. + outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table + partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. + printBaseCounts boolean false Will add base counts to per-locus output. + printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. + start int 1 Starting (left endpoint) for granular binning + stop int 500 Ending (right endpoint) for granular binning + summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. ------ diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -146,12 +146,12 @@ <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /><repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -179,204 +179,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,204 +147,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -407,11 +407,11 @@ **Settings**:: - number int -1 Print the first n reads from the file, discarding the rest - platform String NA Exclude all reads with this platform from the output - readGroup String NA Exclude all reads with this read group from the output - sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times - sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. + number int -1 Print the first n reads from the file, discarding the rest + platform String NA Exclude all reads with this platform from the output + readGroup String NA Exclude all reads with this read group from the output + sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times + sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. ------ diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -134,12 +134,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -165,204 +165,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,204 +154,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -179,12 +179,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -220,204 +220,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -464,13 +464,13 @@ <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" /><param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /> - <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options> - </param> + </param><repeat name="additional_annotations" title="Additional annotation"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> @@ -488,14 +488,14 @@ </when></conditional> --> - <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option> -  - </param> +  + </param><param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,204 +245,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,204 +155,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,204 +211,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,204 +164,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -177,7 +177,7 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> + <option value="dbsnp" selected="True">dbSNP</option><option value="variant">Variants</option><option value="snps">SNPs</option><option value="indels">INDELs</option> @@ -370,204 +370,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,204 +209,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add argument names to parameter help for GATK Advanced options.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5921f5fed6de/ changeset: 5921f5fed6de user: dan date: 2012-04-10 17:20:12 summary: Add argument names to parameter help for GATK Advanced options. affected #: 15 files diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -180,13 +180,13 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="mask">Mask</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /></when> @@ -215,204 +215,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,204 +239,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -996,25 +996,25 @@ **Settings**:: - calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. - ignoreDeletionSites boolean false Ignore sites consisting only of deletions - includeDeletions boolean false Include information on deletions - maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). - maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). - minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. - minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. - nBins int 499 Number of bins to use for granular binning - omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup - omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup - omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup - omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. - outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table - partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. - printBaseCounts boolean false Will add base counts to per-locus output. - printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. - start int 1 Starting (left endpoint) for granular binning - stop int 500 Ending (right endpoint) for granular binning - summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. + calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. + ignoreDeletionSites boolean false Ignore sites consisting only of deletions + includeDeletions boolean false Include information on deletions + maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). + maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). + minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. + minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. + nBins int 499 Number of bins to use for granular binning + omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup + omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup + omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup + omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. + outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table + partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. + printBaseCounts boolean false Will add base counts to per-locus output. + printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. + start int 1 Starting (left endpoint) for granular binning + stop int 500 Ending (right endpoint) for granular binning + summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. ------ diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -146,12 +146,12 @@ <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /><repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -179,204 +179,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,204 +147,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -407,11 +407,11 @@ **Settings**:: - number int -1 Print the first n reads from the file, discarding the rest - platform String NA Exclude all reads with this platform from the output - readGroup String NA Exclude all reads with this read group from the output - sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times - sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. + number int -1 Print the first n reads from the file, discarding the rest + platform String NA Exclude all reads with this platform from the output + readGroup String NA Exclude all reads with this read group from the output + sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times + sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. ------ diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -134,12 +134,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -165,204 +165,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,204 +154,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -179,12 +179,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -220,204 +220,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -464,13 +464,13 @@ <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" /><param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /> - <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options> - </param> + </param><repeat name="additional_annotations" title="Additional annotation"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> @@ -488,14 +488,14 @@ </when></conditional> --> - <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option> -  - </param> +  + </param><param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,204 +245,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,204 +155,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,204 +211,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,204 +164,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -177,7 +177,7 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> + <option value="dbsnp" selected="True">dbSNP</option><option value="variant">Variants</option><option value="snps">SNPs</option><option value="indels">INDELs</option> @@ -370,204 +370,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,204 +209,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0