- galaxy-commits - lists.galaxyproject.org

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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. 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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. 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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. 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