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commit/galaxy-central: jgoecks: Trackster bug fixes when (a) running tools in a shared visualization and (b) when drawing a track created by a tool.
by Bitbucket 19 May '11

19 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7eb9191a9668/ changeset: r5587:7eb9191a9668 user: jgoecks date: 2011-05-19 20:29:58 summary: Trackster bug fixes when (a) running tools in a shared visualization and (b) when drawing a track created by a tool. affected #: 2 files (176 bytes) --- a/static/scripts/trackster.js Thu May 19 13:47:52 2011 -0400 +++ b/static/scripts/trackster.js Thu May 19 14:29:58 2011 -0400 @@ -292,7 +292,7 @@ } */ - // Look for key in cache and, if found, do callback. + // Look for entry and return if found. var entry = this.get(this.gen_key(low, high, mode)); if (entry) { return entry; @@ -1867,6 +1867,10 @@ * tiles after drawing new tiles. */ draw: function(force, clear_after) { + // Cannot draw without dataset_id; dataset_id may not be set if track dynamically created + // and is waiting for dataset. + if (!this.dataset_id) { return; } + var low = this.view.low, high = this.view.high, range = high - low, --- a/templates/visualization/display.mako Thu May 19 13:47:52 2011 -0400 +++ b/templates/visualization/display.mako Thu May 19 14:29:58 2011 -0400 @@ -64,7 +64,7 @@ var default_data_url = "${h.url_for( controller='/tracks', action='data' )}", raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", run_tool_url = "${h.url_for( controller='/tracks', action='run_tool' )}", - rerun_tool_url = "${h.url_for( controller='/tracks', action='run_tool' )}", + rerun_tool_url = "${h.url_for( controller='/tracks', action='rerun_tool' )}", reference_url = "${h.url_for( controller='/tracks', action='reference' )}", chrom_url = "${h.url_for( controller='/tracks', action='chroms' )}", dataset_state_url = "${h.url_for( controller='/tracks', action='dataset_state' )}", 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: jgoecks: Trackster: have child track inherit mode from parent track.
by Bitbucket 19 May '11

19 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3335a0aef0b1/ changeset: r5586:3335a0aef0b1 user: jgoecks date: 2011-05-19 19:47:52 summary: Trackster: have child track inherit mode from parent track. affected #: 2 files (450 bytes) --- a/static/scripts/packed/trackster.js Thu May 19 10:07:53 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu May 19 13:47:52 2011 -0400 @@ -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 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 trackster_module=function(f,S){var n=f("class").extend,p=f("slotting"),H=f("painters");var Y=function(Z,aa){this.document=Z;this.default_font=aa!==undefined?aa:"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")};n(Y.prototype,{load_pattern:function(Z,ad){var aa=this.patterns,ab=this.dummy_context,ac=new Image();ac.src=image_path+ad;ac.onload=function(){aa[Z]=ab.createPattern(ac,"repeat")}},get_pattern:function(Z){return this.patterns[Z]},new_canvas:function(){var Z=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(Z)}Z.manager=this;return Z}});var B=function(Z,aa){Z.bind("drag",{handle:aa,relative:true},function(ae,af){var ad=$(this).parent();var ac=ad.children();var ab;for(ab=0;ab<ac.length;ab++){if(af.offsetY<$(ac.get(ab)).position().top){break}}if(ab===ac.length){if(this!==ac.get(ab-1)){ad.append(this)}}else{if(this!==ac.get(ab)){$(this).insertBefore(ac.get(ab))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};S.sortable=B;var C=9,z=10,N=C+2,w=100,E=12000,L=200,s=10,G=5000,t=100,m="There was an error in indexing this dataset. ",F="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",d=10,r=5,y=5;function u(Z){return Math.round(Z*1000)/1000}var c=function(Z){this.num_elements=Z;this.clear()};n(c.prototype,{get:function(aa){var Z=this.key_ary.indexOf(aa);if(Z!==-1){this.move_key_to_end(aa,Z)}return this.obj_cache[aa]},set:function(aa,ab){if(!this.obj_cache[aa]){if(this.key_ary.length>=this.num_elements){var Z=this.key_ary.shift();delete this.obj_cache[Z]}this.key_ary.push(aa)}this.obj_cache[aa]=ab;return ab},move_key_to_end:function(aa,Z){this.key_ary.splice(Z,1);this.key_ary.push(aa)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var M=function(aa,Z,ab){c.call(this,aa);this.track=Z;this.subset=(ab!==undefined?ab:true)};n(M.prototype,c.prototype,{load_data:function(ah,ai,ad,ag,aa,af){var ac={chrom:ah,low:ai,high:ad,mode:ag,resolution:aa,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ac,af);if(this.track.filters_manager){var aj=[];var Z=this.track.filters_manager.filters;for(var ae=0;ae<Z.length;ae++){aj[aj.length]=Z[ae].name}ac.filter_cols=JSON.stringify(aj)}var ab=this;return $.getJSON(this.track.data_url,ac,function(ak){ab.set_data(ai,ad,ag,ak)})},get_data:function(ab,Z,ae,af,aa,ad){var ac=this.get(this.gen_key(Z,ae,af));if(ac){return ac}ac=this.load_data(ab,Z,ae,af,aa,ad);this.set_data(Z,ae,af,ac);return ac},set_data:function(aa,ab,ac,Z){return this.set(this.gen_key(aa,ab,ac),Z)},gen_key:function(Z,ab,ac){var aa=Z+"_"+ab+"_"+ac;return aa},split_key:function(Z){return Z.split("_")}});var D=function(aa,Z,ab){M.call(this,aa,Z,ab)};n(D.prototype,M.prototype,c.prototype,{load_data:function(ab,Z,ad,ae,aa,ac){if(aa>1){return}return M.prototype.load_data.call(this,ab,Z,ad,ae,aa,ac)}});var X=function(Z,ac,ab,aa,ad){this.container=Z;this.chrom=null;this.vis_id=ab;this.dbkey=aa;this.title=ac;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ad);this.canvas_manager=new Y(Z.get(0).ownerDocument);this.reset()};n(X.prototype,{init:function(ac){var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){Z.zoom_out();Z.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){Z.zoom_in();Z.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ac);this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ad){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.bind("click",function(){for(var ae=0,ad=Z.tracks.length;ae<ad;ae++){Z.tracks[ae].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",Z.overview_box.height());Z.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX),width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.redraw()});this.add_label_track(new W(this,this.top_labeltrack));this.add_label_track(new W(this,this.nav_labeltrack));$(window).bind("resize",function(){Z.resize_window()});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},update_location:function(Z,aa){this.location_span.text(commatize(Z)+" - "+commatize(aa));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(aa))},load_chroms:function(aa,ab){aa.num=t;$.extend(aa,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var Z=this;$.ajax({url:chrom_url,data:aa,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+aa.chrom);return}if(ad.reference){Z.add_label_track(new x(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+t+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+t+"</option>"}Z.chrom_select.html(ag);if(ab){ab()}Z.chrom_start_index=ad.start_index},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}})},change_chrom:function(ad,aa,af){if(!ad||ad==="None"){return}var ac=this;if(ad==="previous"){ac.load_chroms({low:this.chrom_start_index-t});return}if(ad==="next"){ac.load_chroms({low:this.chrom_start_index+t});return}var ae=$.grep(ac.chrom_data,function(ah,ai){return ah.chrom===ad})[0];if(ae===undefined){ac.load_chroms({chrom:ad},function(){ac.change_chrom(ad,aa,af)});return}else{if(ad!==ac.chrom){ac.chrom=ad;if(!ac.chrom){ac.intro_div.show()}else{ac.intro_div.hide()}ac.chrom_select.val(ac.chrom);ac.max_high=ae.len-1;ac.reset();ac.redraw(true);for(var ag=0,Z=ac.tracks.length;ag<Z;ag++){var ab=ac.tracks[ag];if(ab.init){ab.init()}}}if(aa!==undefined&&af!==undefined){ac.low=Math.max(aa,0);ac.high=Math.min(af,ac.max_high)}ac.reset_overview();ac.redraw()}},go_to:function(ad){var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0].replace(/,/g,""),10);ac=parseInt(ae[1].replace(/,/g,""),10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ab){var Z=this;var aa=Z.high-Z.low;if(Z.low-ab<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+aa}else{if(Z.high-ab>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-aa}else{Z.high-=ab;Z.low-=ab}}Z.redraw()},add_track:function(Z){Z.view=this;Z.track_id=this.track_id_counter;this.tracks.push(Z);if(Z.init){Z.init()}Z.container_div.attr("id","track_"+Z.track_id);B(Z.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(Z){Z.view=this;this.label_tracks.push(Z)},remove_track:function(Z){this.has_changes=true;Z.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(Z)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ag){var af=this.high-this.low,ae=this.low,aa=this.high;if(ae<this.max_low){ae=this.max_low}if(aa>this.max_high){aa=this.max_high}if(this.high!==0&&af<this.min_separation){aa=ae+this.min_separation}this.low=Math.floor(ae);this.high=Math.ceil(aa);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/L)/Math.LN10));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=13;this.overview_box.css({left:Z,width:Math.max(ah,ad)}).show();if(ad<ah){this.overview_box.css("left",Z-(ah-ad)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:ad})}this.update_location(this.low,this.high);if(!ag){for(var ab=0,ac=this.tracks.length;ab<ac;ab++){if(this.tracks[ab]&&this.tracks[ab].enabled){this.tracks[ab].draw()}}for(ab=0,ac=this.label_tracks.length;ab<ac;ab++){this.label_tracks[ab].draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var o=function(ab,af){this.track=ab;this.name=af.name;this.params=[];var am=af.params;for(var ac=0;ac<am.length;ac++){var ah=am[ac],aa=ah.name,al=ah.label,ad=unescape(ah.html),an=ah.value,aj=ah.type;if(aj==="number"){this.params[this.params.length]=new g(aa,al,ad,an,ah.min,ah.max)}else{if(aj=="select"){this.params[this.params.length]=new J(aa,al,ad,an)}else{console.log("WARNING: unrecognized tool parameter type:",aa,aj)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ap){ap.stopPropagation()}).bind("click",function(ap){ap.stopPropagation()}).bind("dblclick",function(ap){ap.stopPropagation()});var ak=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ai=this.params;var ag=this;$.each(this.params,function(aq,au){var at=$("<div>").addClass("param-row").appendTo(ag.parent_div);var ap=$("<div>").addClass("param-label").text(au.label).appendTo(at);var ar=$("<div/>").addClass("slider").html(au.html).appendTo(at);ar.find(":input").val(au.value);$("<div style='clear: both;'/>").appendTo(at)});this.parent_div.find("input").click(function(){$(this).select()});var ao=$("<div>").addClass("param-row").appendTo(this.parent_div);var ae=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ao);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ao);var ag=this;Z.click(function(){ag.run_on_region()});ae.click(function(){ag.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=JSON.stringify(ab)});return Z},get_param_values:function(){var aa=[];var Z={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();if(ab){aa[aa.length]=ac}});return aa},run_on_dataset:function(){var Z=this;Z.run({dataset_id:this.track.original_dataset_id,tool_id:Z.name},function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var Z={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},ab=this.track,aa=Z.tool_id+ab.tool_region_and_parameters_str(Z.chrom,Z.low,Z.high),ac;if(ab.track_type==="FeatureTrack"){ac=new P(aa,view,ab.hda_ldda,undefined,{},{},ab)}this.track.add_track(ac);ac.content_div.text("Starting job.");this.run(Z,function(ad){ac.dataset_id=ad.dataset_id;ac.content_div.text("Running job.");ac.init()})},run:function(aa,ab){$.extend(aa,this.get_param_values_dict());var Z=function(){$.getJSON(rerun_tool_url,aa,function(ac){if(ac==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(F)}else{if(ac.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ac.message)}else{if(ac==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(Z,2000)}else{ab(ac)}}}})};Z()}});var J=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=ab;this.value=ac};var g=function(ab,aa,ad,ae,ac,Z){J.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};var h=function(aa,Z,ab,ac){this.name=aa;this.index=Z;this.tool_id=ab;this.tool_exp_name=ac};var Q=function(aa,Z,ab,ac){h.call(this,aa,Z,ab,ac);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(Q.prototype,{applies_to:function(Z){if(Z.length>this.index){return true}return false},keep:function(Z){if(!this.applies_to(Z)){return true}var aa=parseInt(Z[this.index]);return(isNaN(aa)||(aa>=this.low&&aa<=this.high))},update_attrs:function(aa){var Z=false;if(!this.applies_to(aa)){return Z}if(aa[this.index]<this.min){this.min=Math.floor(aa[this.index]);Z=true}if(aa[this.index]>this.max){this.max=Math.ceil(aa[this.index]);Z=true}return Z},update_ui_elt:function(){var ab=function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)};var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ab(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ak){this.track=ab;this.filters=[];for(var af=0;af<ak.length;af++){var Z=ak[af],aa=Z.name,aj=Z.type,ah=Z.index,am=Z.tool_id,ac=Z.tool_exp_name;if(aj==="int"||aj==="float"){this.filters[af]=new Q(aa,ah,am,ac)}else{console.log("ERROR: unsupported filter: ",aa,aj)}}var ai=function(an,ao,ap){an.click(function(){var aq=ao.text();max=parseFloat(ap.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ap.slider("option","values")){input_size=2*input_size+1;multi_value=true}ao.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aq).appendTo(ao).focus().select().click(function(ar){ar.stopPropagation()}).blur(function(){$(this).remove();ao.text(aq)}).keyup(function(aw){if(aw.keyCode===27){$(this).trigger("blur")}else{if(aw.keyCode===13){var au=ap.slider("option","min"),ar=ap.slider("option","max"),av=function(ax){return(isNaN(ax)||ax>ar||ax<au)},at=$(this).val();if(!multi_value){at=parseFloat(at);if(av(at)){alert("Parameter value must be in the range ["+au+"-"+ar+"]");return $(this)}}else{at=at.split("-");at=[parseFloat(at[0]),parseFloat(at[1])];if(av(at[0])||av(at[1])){alert("Parameter value must be in the range ["+au+"-"+ar+"]");return $(this)}}ap.slider((multi_value?"values":"value"),at)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(an){an.stopPropagation()}).bind("click",function(an){an.stopPropagation()}).bind("dblclick",function(an){an.stopPropagation()}).bind("keydown",function(an){an.stopPropagation()});var ad=this;$.each(this.filters,function(au,ao){var aq=$("<div/>").addClass("slider-row").appendTo(ad.parent_div);var an=$("<div/>").addClass("slider-label").appendTo(aq);var aw=$("<span/>").addClass("slider-name").text(ao.name+" ").appendTo(an);var ap=$("<span/>");var ar=$("<span/>").addClass("slider-value").appendTo(an).append("[").append(ap).append("]");var av=$("<div/>").addClass("slider").appendTo(aq);ao.control_element=$("<div/>").attr("id",ao.name+"-filter-control").appendTo(av);var at=[0,0];ao.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ax,ay){at=ay.values;ap.text(ay.values[0]+"-"+ay.values[1]);setTimeout(function(){if(ay.values[0]==at[0]&&ay.values[1]==at[1]){var az=ay.values;ap.text(az[0]+"-"+az[1]);ao.low=az[0];ao.high=az[1];ad.track.draw(true,true)}},50)},change:function(ax,ay){ao.control_element.slider("option","slide").call(ao.control_element,ax,ay)}});ao.slider=ao.control_element;ao.slider_label=ap;ai(ar,ap,ao.control_element);$("<div style='clear: both;'/>").appendTo(aq)});if(this.filters.length!=0){var al=$("<div>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(al);var ae=this;ag.click(function(){ae.run_on_dataset()})}};n(V.prototype,{reset_filters:function(){for(var Z=0;Z<this.filters.length;Z++){filter=this.filters[Z];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ah=function(al,aj,ak){if(!(aj in al)){al[aj]=ak}return al[aj]};var ab={},Z,aa,ac;for(var ad=0;ad<this.filters.length;ad++){Z=this.filters[ad];if(Z.tool_id){if(Z.min!=Z.low){aa=ah(ab,Z.tool_id,[]);aa[aa.length]=Z.tool_exp_name+" >= "+Z.low}if(Z.max!=Z.high){aa=ah(ab,Z.tool_id,[]);aa[aa.length]=Z.tool_exp_name+" <= "+Z.high}}}var af=[];for(var ai in ab){af[af.length]=[ai,ab[ai]]}var ag=af.length;(function ae(ap,am){var ak=am[0],al=ak[0],ao=ak[1],an="("+ao.join(") and (")+")",aj={cond:an,input:ap,target_dataset_id:ap,tool_id:al},am=am.slice(1);$.getJSON(run_tool_url,aj,function(aq){if(aq.error){show_modal("Filter Dataset","Error running tool "+al,{Close:hide_modal})}else{if(am.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ae(aq.dataset_id,am)}}})})(this.track.dataset_id,af)}});var U=function(Z){this.track=Z.track;this.params=Z.params;this.values={};if(Z.saved_values){this.restore_values(Z.saved_values)}this.onchange=Z.onchange};n(U.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var aa=this;var Z=$("<div />");$.each(this.params,function(ae,ac){if(!ac.hidden){var ab="param_"+ae;var aj=$("<div class='form-row' />").appendTo(Z);aj.append($("<label />").attr("for",ab).text(ac.label+":"));if(ac.type==="bool"){aj.append($('<input type="checkbox" />').attr("id",ab).attr("name",ab).attr("checked",aa.values[ac.key]))}else{if(ac.type==="color"){var ag=aa.values[ac.key];var af=$("<input />").attr("id",ab).attr("name",ab).val(ag);var ah=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ad=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ah);var ai=$("<div/>").appendTo(ad).farbtastic({width:100,height:100,callback:af,color:ag});$("<div />").append(af).append(ah).appendTo(aj).bind("click",function(ak){ah.css({left:$(this).position().left+($(af).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ah.hide();$(document).unbind("click.color-picker")});ak.stopPropagation()})}else{aj.append($("<input />").attr("id",ab).attr("name",ab).val(aa.values[ac.key]))}}}});return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange()}}});var b=function(ab,aa,Z){this.index=ab;this.resolution=aa;this.canvas=$("<div class='track-tile'/>").append(Z)};var l=function(ab,aa,Z,ac){b.call(this,ab,aa,Z);this.max_val=ac};var K=function(ab,aa,Z){b.call(this,ab,aa,Z)};var j=function(aa,Z,ad,ab,ac){this.name=aa;this.view=Z;this.parent_element=ad;this.data_url=(ab?ab:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ac?ac:G);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{init:function(){var Z=this;Z.enabled=false;Z.tile_cache.clear();Z.data_cache.clear();Z.initial_canvas=undefined;Z.content_div.css("height","auto");Z.container_div.removeClass("nodata error pending");if(!Z.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id,chrom:Z.view.chrom},function(aa){if(!aa||aa==="error"||aa.kind==="error"){Z.container_div.addClass("error");Z.content_div.text(m);if(aa.message){var ac=Z.view.tracks.indexOf(Z);var ab=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+aa.message+"</pre>",{Close:hide_modal})});Z.content_div.append(ab)}}else{if(aa==="no converter"){Z.container_div.addClass("error");Z.content_div.text(F)}else{if(aa==="no data"||(aa.data!==undefined&&(aa.data===null||aa.data.length===0))){Z.container_div.addClass("nodata");Z.content_div.text(A)}else{if(aa==="pending"){Z.container_div.addClass("pending");Z.content_div.text(q);setTimeout(function(){Z.init()},Z.data_query_wait)}else{if(aa.status==="data"){if(aa.valid_chroms){Z.valid_chroms=aa.valid_chroms;Z.make_name_popup_menu()}Z.content_div.text(T);if(Z.view.chrom){Z.content_div.text("");Z.content_div.css("height",Z.height_px+"px");Z.enabled=true;$.when(Z.predraw_init()).done(function(){Z.container_div.removeClass("nodata error pending");Z.draw()})}}}}}}})},predraw_init:function(){},update_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var I=function(ah,af,ai){var aa=this,aj=aa.view;this.filters_manager=(ah!==undefined?new V(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(aa.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}aa.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();aa.container_div.append(aa.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(aa.display_modes!==undefined){if(aa.mode_div===undefined){aa.mode_div=$("<div class='right-float menubutton popup' />").appendTo(aa.header_div);var ac=(aa.track_config&&aa.track_config.values.mode?aa.track_config.values.mode:aa.display_modes[0]);aa.mode=ac;aa.mode_div.text(ac);var ab=function(ak){aa.mode_div.text(ak);aa.mode=ak;aa.track_config.values.mode=ak;aa.tile_cache.clear();aa.draw()};var Z={};for(var ad=0,ag=aa.display_modes.length;ad<ag;ad++){var ae=aa.display_modes[ad];Z[ae]=function(ak){return function(){ab(ak)}}(ae)}make_popupmenu(aa.mode_div,Z)}else{aa.mode_div.hide()}}this.make_name_popup_menu()};n(I.prototype,j.prototype,{make_name_popup_menu:function(){var aa=this;var Z={};Z["Edit configuration"]=function(){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){aa.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure Track",aa.track_config.build_form(),{Cancel:ag,OK:ae})};if(aa.filters_available>0){var ad=(aa.filters_div.is(":visible")?"Hide filters":"Show filters");Z[ad]=function(){aa.filters_visible=(aa.filters_div.is(":visible"));if(aa.filters_visible){aa.filters_manager.reset_filters()}aa.filters_div.toggle();aa.make_name_popup_menu()}}if(aa.tool){var ad=(aa.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");Z[ad]=function(){if(!aa.dynamic_tool_div.is(":visible")){aa.update_name(aa.name+aa.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";aa.revert_name()}aa.dynamic_tool_div.toggle();aa.make_name_popup_menu()}}if(aa.valid_chroms){Z["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+aa.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ab=view;var ac=function(){$("#no-tracks").show()};if(this.parent_track){ab=this.parent_track;ac=function(){}}Z.Remove=function(){ab.remove_track(aa);if(ab.num_tracks===0){ac()}};make_popupmenu(aa.name_div,Z)},draw:function(Z,ab){var at=this.view.low,af=this.view.high,ah=af-at,aj=this.view.container.width(),ad=aj/ah,ak=this.view.resolution,ac=$("<div style='position: relative;'></div>"),al=function(av,aw,au){return av+"_"+aw+"_"+au};if(!ab){this.content_div.children().remove()}this.content_div.append(ac);this.max_height=0;var an=Math.floor(at/ak/L);var ae=[];var ao=0;while((an*L*ak)<af){var ar=al(aj,ad,an);var ag=this.tile_cache.get(ar);var ap=an*L*this.view.resolution;var aa=ap+L*this.view.resolution;if(!Z&&ag){ae[ae.length]=ag;this.show_tile(ag,ac,ap,ad)}else{this.delayed_draw(Z,ar,an,ak,ac,ad,ae)}an+=1;ao++}var ai=this;var aq=setInterval(function(){if(ae.length===ao){clearInterval(aq);if(ab){var ax=ai.content_div.children();var ay=false;for(var aw=ax.length-1,aC=0;aw>=aC;aw--){var av=$(ax[aw]);if(ay){av.remove()}else{if(av.children().length!==0){ay=true}}}}if(ai.track_type=="FeatureTrack"&&ai.mode=="Histogram"){var aB=-1;for(var aw=0;aw<ae.length;aw++){var aE=ae[aw].max_val;if(aE>aB){aB=aE}}for(var aw=0;aw<ae.length;aw++){if(ae[aw].max_val!==aB){var aD=ae[aw];aD.canvas.remove();ai.delayed_draw(true,al(aj,ad,aD.index),aD.index,aD.resolution,ac,ad,[],{max:aB})}}}if(ai.filters_manager){var au=ai.filters_manager.filters;for(var aA=0;aA<au.length;aA++){au[aA].update_ui_elt()}var az=false;if(ai.example_feature){for(var aA=0;aA<au.length;aA++){if(au[aA].applies_to(ai.example_feature)){az=true;break}}}if(ai.filters_available!==az){ai.filters_available=az;if(!ai.filters_available){ai.filters_div.hide()}ai.make_name_popup_menu()}}}},50);for(var am=0;am<this.child_tracks.length;am++){this.child_tracks[am].draw(Z,ab)}},delayed_draw:function(aa,ah,ab,ad,ai,al,aj,ae){var ac=this,af=ab*L*ad,ak=af+L*ad;var ag=function(au,am,ao,an,ar,at,ap){var aq=ac.draw_tile(am,ao,an,at,ap);ac.tile_cache.set(ah,aq);if(aq===undefined){return}ac.show_tile(aq,ar,af,at);aj[aj.length]=aq};var Z=setTimeout(function(){if(af<=ac.view.high&&ak>=ac.view.low){var am=(aa?undefined:ac.tile_cache.get(ah));if(am){ac.show_tile(am,ai,af,al);aj[aj.length]=am}else{$.when(ac.data_cache.get_data(view.chrom,af,ak,ac.mode,ad,ac.data_url_extra_params)).then(function(an){n(an,ae);if(view.reference_track&&al>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,af,ak,ac.mode,ad,view.reference_track.data_url_extra_params)).then(function(ao){ag(Z,an,ad,ab,ai,al,ao)})}else{ag(Z,an,ad,ab,ai,al)}})}}},50)},show_tile:function(ac,af,ad,ag){var aa=this;var ab=this.view.high-this.view.low,ae=(ad-this.view.low)*ag;if(this.left_offset){ae-=this.left_offset}var Z=ac.canvas;Z.css({position:"absolute",top:0,left:ae,height:""});af.append(Z);aa.max_height=Math.max(aa.max_height,Z.height());aa.content_div.css("height",aa.max_height+"px");af.children().css("height",aa.max_height+"px")},set_overview:function(){var Z=this.view;if(this.initial_canvas&&this.is_overview){Z.overview_close.show();Z.overview_viewport.append(this.initial_canvas);Z.overview_highlight.show().height(this.initial_canvas.height());Z.overview_viewport.height(this.initial_canvas.height()+Z.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},add_track:function(Z){Z.track_id=this.track_id+"_"+this.child_tracks.length;Z.container_div.attr("id","track_"+Z.track_id);this.child_tracks_container.append(Z.container_div);B(Z.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(Z);this.view.has_changes=true},remove_track:function(Z){Z.container_div.fadeOut("slow",function(){$(this).remove()})}});var W=function(Z,aa){this.track_type="LabelTrack";this.hidden=true;j.call(this,null,Z,aa);this.container_div.addClass("label-track")};n(W.prototype,j.prototype,{draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var x=function(Z){this.track_type="ReferenceTrack";this.hidden=true;j.call(this,null,Z,Z.top_labeltrack);I.call(this);Z.reference_track=this;this.left_offset=200;this.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:Z.dbkey};this.data_cache=new D(y,this,false);this.tile_cache=new c(r)};n(x.prototype,I.prototype,{draw_tile:function(ah,ae,aa,aj){var ad=this,ab=L*ae;if(aj>this.view.canvas_manager.char_width_px){if(ah===null){ad.content_div.css("height","0px");return}var ac=this.view.canvas_manager.new_canvas();var ai=ac.getContext("2d");ac.width=Math.ceil(ab*aj+ad.left_offset);ac.height=ad.height_px;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";for(var af=0,ag=ah.length;af<ag;af++){var Z=Math.round(af*aj);ai.fillText(ah[af],Z+ad.left_offset,10)}return new b(aa,ae,ac)}this.content_div.css("height","0px")}});var k=function(ad,ab,ae,Z,ac){var aa=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ad,ab,ab.viewport_container);I.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ae;this.dataset_id=Z;this.original_dataset_id=Z;this.data_cache=new M(y,this);this.tile_cache=new c(r);this.track_config=new U({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:ac,onchange:function(){aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;$("#linetrack_"+aa.track_id+"_minval").text(aa.prefs.min_value);$("#linetrack_"+aa.track_id+"_maxval").text(aa.prefs.max_value);aa.tile_cache.clear();aa.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,I.prototype,{add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){ac=true;aa.show()},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.content_div).css("height",ad);Z.height_px=ad;Z.draw(true)}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.track_config.values.height=Z.height_px}).appendTo(Z.container_div)},predraw_init:function(){var Z=this,aa=Z.view.tracks.indexOf(Z);Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:null,high:null,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(ab){Z.container_div.addClass("line-track");var ad=ab.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){Z.prefs.min_value=ad.min;Z.prefs.max_value=ad.max;$("#track_"+aa+"_minval").val(Z.prefs.min_value);$("#track_"+aa+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+aa+"_minval").text(u(Z.prefs.min_value));var ac=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+aa+"_maxval").text(u(Z.prefs.max_value));ac.css({position:"absolute",top:"24px",left:"10px"});ac.prependTo(Z.container_div);ae.css({position:"absolute",bottom:"2px",left:"10px"});ae.prependTo(Z.container_div)})},draw_tile:function(aj,ad,aa,ai){if(this.vertical_range===undefined){return}var ae=aa*L*ad,ac=L*ad,Z=Math.ceil(ac*ai),ag=this.height_px;var ab=this.view.canvas_manager.new_canvas();ab.width=Z,ab.height=ag;var ah=ab.getContext("2d");var af=new H.LinePainter(aj.data,ae,ae+ac,this.prefs,this.mode);af.draw(ah,Z,ag);return new b(ac,ad,ab)}});var e=function(Z,ae,ad,ah,ag,ab,ac,af){var aa=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new U({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag,onchange:function(){aa.tile_cache.clear();aa.draw()}});this.prefs=this.track_config.values;j.call(this,Z,ae,ae.viewport_container);I.call(this,ab,ac,af);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ad;this.dataset_id=ah;this.original_dataset_id=ah;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new M(20,this);this.left_offset=200;this.painter=H.LinkedFeaturePainter};n(e.prototype,I.prototype,{update_auto_mode:function(Z){if(this.mode=="Auto"){if(Z=="no_detail"){Z="feature spans"}else{if(Z=="summary_tree"){Z="coverage histogram"}}this.mode_div.text("Auto ("+Z+")")}},incremental_slots:function(ad,aa,ac){var ab=this.view.canvas_manager.dummy_context,Z=this.inc_slots[ad];if(!Z||(Z.mode!==ac)){Z=new (p.FeatureSlotter)(ad,ac==="Pack",w,function(ae){return ab.measureText(ae)});Z.mode=ac;this.inc_slots[ad]=Z}return Z.slot_features(aa)},get_summary_tree_data:function(ad,ag,ab,ao){if(ao>ab-ag){ao=ab-ag}var ak=Math.floor((ab-ag)/ao),an=[],ac=0;var ae=0,af=0,aj,am=0,ah=[],al,ai;var aa=function(ar,aq,at,ap){ar[0]=aq+at*ap;ar[1]=aq+(at+1)*ap};while(am<ao&&ae!==ad.length){var Z=false;for(;am<ao&&!Z;am++){aa(ah,ag,am,ak);for(af=ae;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){Z=true;break}}if(Z){break}}data_start_index=af;an[an.length]=al=[ah[0],0];for(;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){al[1]++}else{break}}if(al[1]>ac){ac=al[1]}am++}return{max:ac,delta:ak,data:an}},draw_tile:function(am,av,az,ai,ac){var ar=this,aB=az*L*av,aa=(az+1)*L*av,ao=aa-aB,at=Math.ceil(ao*ai),aq=this.mode,aF=25,ad=this.left_offset,an,ae;if(aq==="Auto"){if(am.dataset_type==="summary_tree"){aq=am.dataset_type}else{if(am.extra_info==="no_detail"){aq="no_detail"}else{var aE=am.data;if(this.view.high-this.view.low>E){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){ae=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var Z=$("<div />").addClass("yaxislabel");Z.text(am.max);Z.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});Z.prependTo(this.container_div);var ab=this.view.canvas_manager.new_canvas();ab.width=at+ad;ab.height=ae+N;if(am.dataset_type!="summary_tree"){var aj=this.get_summary_tree_data(am.data,aB,aa,200);if(am.max){aj.max=am.max}am=aj}var aC=new H.SummaryTreePainter(am,aB,aa,this.prefs);var au=ab.getContext("2d");au.translate(ad,N);aC.draw(au,at,ae);return new l(az,av,ab,am.max)}var an,ag=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ag=this.incremental_slots(ai,am.data,aq);an=this.inc_slots[ai].slots}var ah=[];if(am.data){var ak=this.filters_manager.filters;for(var aw=0,ay=am.data.length;aw<ay;aw++){var af=am.data[aw];var ax=false;var al;for(var aA=0,aD=ak.length;aA<aD;aA++){al=ak[aA];al.update_attrs(af);if(!al.keep(af)){ax=true;break}}if(!ax){ah.push(af)}}}var aC=new (this.painter)(ah,aB,aa,this.prefs,aq,ac);var ae=aC.get_required_height(ag)+z;var ab=this.view.canvas_manager.new_canvas();ab.width=at+ad;ab.height=ae;var au=ab.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(am.message){au.fillStyle="red";au.textAlign="left";var ap=au.textBaseline;au.textBaseline="top";au.fillRect(ad,0,ab.width-ad,1);au.fillText(am.message,ad,2);au.textBaseline=ap;if(!am.data){return new b(az,av,ab,ae)}}this.example_feature=(am.data.length?am.data[0]:undefined);au.translate(ad,z);aC.draw(au,at,ae,an);return new K(az,av,ab)}});var O=function(ac,aa,ae,Z,ab,ad){e.call(this,ac,aa,ae,Z,ab,ad);this.track_type="VcfTrack";this.painter=H.VariantPainter};n(O.prototype,I.prototype,e.prototype);var R=function(ac,aa,ae,Z,ab,ad){e.call(this,ac,aa,ae,Z,ab,ad);this.track_config=new U({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ab,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=H.ReadPainter;this.make_name_popup_menu()};n(R.prototype,I.prototype,e.prototype);var P=function(ad,ab,af,Z,ac,ae,aa){e.call(this,ad,ab,af,Z,ac,ae,{},aa);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(P.prototype,I.prototype,e.prototype,{predraw_init:function(){var aa=this;var Z=function(){if(aa.data_cache.size()===0){setTimeout(Z,300)}else{aa.data_url=default_data_url;aa.data_query_wait=G;aa.dataset_state_url=converted_datasets_state_url;$.getJSON(aa.dataset_state_url,{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},function(ab){})}};Z()}});S.View=X;S.LineTrack=k;S.FeatureTrack=e;S.ReadTrack=R};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(O,N,L){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,K=D-H,z=L,A=this.view_start,M=this.view_end-this.view_start,B=N/M,I=this.mode,S=this.data;O.save();var T=Math.round(L+H/K*L);if(I!=="Intensity"){O.fillStyle="#aaa";O.fillRect(0,T,N,1)}O.beginPath();O.fillStyle=this.prefs.color;var R,E,C;if(S.length>1){C=Math.ceil((S[1][0]-S[0][0])*B)}else{C=10}for(var P=0,Q=S.length;P<Q;P++){R=Math.round((S[P][0]-A)*B);E=S[P][1];if(E===null){if(F&&I==="Filled"){O.lineTo(R,z)}F=false;continue}if(E<H){E=H}else{if(E>D){E=D}}if(I==="Histogram"){E=Math.round(E/K*z);O.fillRect(R,T,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/K*255);O.fillStyle="rgb("+E+","+E+","+E+")";O.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/K*z);if(F){O.lineTo(R,E)}else{F=true;if(I==="Filled"){O.moveTo(R,z);O.lineTo(R,E)}else{O.moveTo(R,E)}}}}}if(I==="Filled"){if(F){O.lineTo(R,T);O.lineTo(0,T)}O.fill()}else{O.stroke()}var x=-1,J=-1;O.fillStyle=this.prefs.overflow_color;var G;for(var P=0,Q=S.length;P<Q;P++){E=S[P][1];R=Math.round((S[P][0]-A)*B);if(J>=0&&(E===null||E<D)){O.fillRect(J,0,G+C-J,2);J=-1}else{if(x>=0&&(E===null||E>H)){O.fillRect(x,L-2,G+C-x,2);x=-1}}if(E!==null&&E>D&&J<0){J=R}else{if(E!==null&&E<H&&x<0){x=R}}G=R}O.restore()};var n=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,A,I,F){var D=this.data,G=this.view_start,K=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var N=this.view_end-this.view_start,M=A/N,z=this.get_row_height();for(var C=0,E=D.length;C<E;C++){var L=D[C],B=L[0],x=L[1],y=L[2],H=(F&&F[B]!==undefined?F[B]:null);if((x<K&&y>G)&&(this.mode=="Dense"||H!==null)){this.draw_element(J,this.mode,L,H,G,K,M,z,A)}}J.restore()}});var d=10,h=3,l=5,v=10,f=1,r=3,e=3,a=9,k=2,g="#ccc";var q=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=d}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=l}else{x=v}}}return x},draw_element:function(J,C,R,E,L,ab,af,ag,x){var O=R[0],ad=R[1],V=R[2],M=R[3],W=Math.floor(Math.max(0,(ad-L)*af)),K=Math.ceil(Math.min(x,Math.max(0,(V-L)*af))),U=(C==="Dense"?0:(0+E))*ag,I,Z,N=null,ah=null,A=this.prefs.block_color,Y=this.prefs.label_color;if(C=="Dense"){E=1}if(C==="no_detail"){J.fillStyle=A;J.fillRect(W,U+5,K-W,f)}else{var H=R[4],T=R[5],X=R[6],B=R[7];if(T&&X){N=Math.floor(Math.max(0,(T-L)*af));ah=Math.ceil(Math.min(x,Math.max(0,(X-L)*af)))}var ae,P;if(C==="Squish"||C==="Dense"){ae=1;P=e}else{ae=5;P=a}if(!B){if(R.strand){if(R.strand==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(R.strand==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}}else{J.fillStyle=A}J.fillRect(W,U,K-W,P)}else{var G,Q;if(C==="Squish"||C==="Dense"){J.fillStyle=g;G=U+Math.floor(e/2)+1;Q=1}else{if(H){var G=U;var Q=P;if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand")}}}else{J.fillStyle=g;G+=(e/2)+1;Q=1}}J.fillRect(W,G,K-W,Q);for(var ac=0,z=B.length;ac<z;ac++){var D=B[ac],y=Math.floor(Math.max(0,(D[0]-L)*af)),S=Math.ceil(Math.min(x,Math.max((D[1]-L)*af)));if(y>S){continue}J.fillStyle=A;J.fillRect(y,U+(P-ae)/2+1,S-y,ae);if(N!==undefined&&X>T&&!(y>ah||S<N)){var aa=Math.max(y,N),F=Math.min(S,ah);J.fillRect(aa,U+1,F-aa,P);if(B.length==1&&C=="Pack"){if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}if(aa+14<F){aa+=2;F-=2}J.fillRect(aa,U+1,F-aa,P)}}}}if(C==="Pack"&&ad>L){J.fillStyle=Y;if(L===0&&W-J.measureText(M).width<0){J.textAlign="left";J.fillText(M,K+k,U+8)}else{J.textAlign="right";J.fillText(M,W-k,U+8)}J.fillStyle=A}}}});var b=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(b.prototype,n.prototype,{draw_element:function(Q,L,F,B,T,z,I,R,O){var F=data[i],H=F[0],P=F[1],A=F[2],K=F[3],D=Math.floor(Math.max(0,(P-T)*I)),G=Math.ceil(Math.min(O,Math.max(0,(A-T)*I))),C=(L==="Dense"?0:(0+B))*R,x,U,y=null,J=null;if(no_label){Q.fillStyle=block_color;Q.fillRect(D+left_offset,C+5,G-D,1)}else{var S=F[4],N=F[5],E=F[6];x=9;U=1;Q.fillRect(D+left_offset,C,G-D,x);if(L!=="Dense"&&K!==undefined&&P>T){Q.fillStyle=label_color;if(T===0&&D-Q.measureText(K).width<0){Q.textAlign="left";Q.fillText(K,G+2+left_offset,C+8)}else{Q.textAlign="right";Q.fillText(K,D-2+left_offset,C+8)}Q.fillStyle=block_color}var M=S+" / "+N;if(P>T&&Q.measureText(M).width<(G-D)){Q.fillStyle="white";Q.textAlign="center";Q.fillText(M,left_offset+D+(G-D)/2,C+8);Q.fillStyle=block_color}}}});var s=function(A,C,x,z,B,y){n.call(this,A,C,x,z,B);this.ref_seq=y};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=d}else{if(y==="Squish"){x=l}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(T,O,K,Y,z,S,H,E,D){T.textAlign="center";var R=this,y=[Y,z],N=0,U=0,Q=0;ref_seq=this.ref_seq,char_width_px=T.canvas.manager.char_width_px;var ad=[];if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){Q=Math.round(K/2)}if(!H){H=[[0,E.length]]}for(var L=0,W=H.length;L<W;L++){var I=H[L],A="MIDNSHP=X"[I[0]],M=I[1];if(A==="H"||A==="S"){N-=M}var F=S+N,ac=Math.floor(Math.max(0,(F-Y)*K)),G=Math.floor(Math.max(0,(F+M-Y)*K));if(ac===G){G+=1}switch(A){case"H":break;case"S":case"M":case"=":if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(Q>0){T.fillStyle=this.prefs.block_color;T.fillRect(ac-Q,D+1,G-ac,9);T.fillStyle=g;for(var aa=0,x=P.length;aa<x;aa++){if(this.prefs.show_differences&&ref_seq){var J=ref_seq[F-Y+aa];if(!J||J.toLowerCase()===P[aa].toLowerCase()){continue}}if(F+aa>=Y&&F+aa<=z){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab,D+9)}}}else{T.fillStyle=this.prefs.block_color;T.fillRect(ac,D+4,G-ac,e)}}U+=M;N+=M;break;case"N":T.fillStyle=g;T.fillRect(ac-Q,D+5,G-ac,1);N+=M;break;case"D":T.fillStyle="red";T.fillRect(ac-Q,D+4,G-ac,3);N+=M;break;case"P":break;case"I":var X=ac-Q;if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(this.prefs.show_insertions){var C=ac-(G-ac)/2;if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){T.fillStyle="yellow";T.fillRect(C-Q,D-9,G-ac,9);ad[ad.length]={type:"triangle",data:[X,D+4,5]};T.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):P=P.slice(Y-F);break;case (OVERLAP_END):P=P.slice(0,F-z);break;case (CONTAINED_BY):break;case (CONTAINS):P=P.slice(Y-F,F-z);break}for(var aa=0,x=P.length;aa<x;aa++){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab-(G-ac)/2,D)}}else{T.fillStyle="yellow";T.fillRect(C,D+(this.mode!=="Dense"?2:5),G-ac,(O!=="Dense"?e:r))}}else{if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){ad[ad.length]={type:"text",data:[P.length,X,D+9]}}else{}}}U+=M;break;case"X":U+=M;break}}T.fillStyle="yellow";var Z,B,ae;for(var V=0;V<ad.length;V++){Z=ad[V];B=Z.type;ae=Z.data;if(B==="text"){T.save();T.font="bold 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S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+k-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-k-N,B+8)}Q.fillStyle=U}}});w.SummaryTreePainter=u;w.LinePainter=c;w.LinkedFeaturePainter=q;w.ReadPainter=s;w.VariantPainter=b};(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 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 trackster_module=function(f,T){var n=f("class").extend,p=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"9px Monaco, Lucida Console, 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ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};T.sortable=C;var D=9,A=10,O=D+2,w=100,F=12000,M=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",d=10,r=5,y=5;function u(aa){return Math.round(aa*1000)/1000}var c=function(aa){this.num_elements=aa;this.clear()};n(c.prototype,{get:function(ab){var aa=this.key_ary.indexOf(ab);if(aa!==-1){this.move_key_to_end(ab,aa)}return this.obj_cache[ab]},set:function(ab,ac){if(!this.obj_cache[ab]){if(this.key_ary.length>=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};n(N.prototype,c.prototype,{load_data:function(ai,aj,ae,ah,ab,ag){var ad={chrom:ai,low:aj,high:ae,mode:ah,resolution:ab,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ad,ag);if(this.track.filters_manager){var ak=[];var aa=this.track.filters_manager.filters;for(var af=0;af<aa.length;af++){ak[ak.length]=aa[af].name}ad.filter_cols=JSON.stringify(ak)}var ac=this;return $.getJSON(this.track.data_url,ad,function(al){ac.set_data(aj,ae,ah,al)})},get_data:function(ac,aa,af,ag,ab,ae){var ad=this.get(this.gen_key(aa,af,ag));if(ad){return ad}ad=this.load_data(ac,aa,af,ag,ab,ae);this.set_data(aa,af,ag,ad);return ad},set_data:function(ab,ac,ad,aa){return this.set(this.gen_key(ab,ac,ad),aa)},gen_key:function(aa,ac,ad){var ab=aa+"_"+ac+"_"+ad;return ab},split_key:function(aa){return aa.split("_")}});var E=function(ab,aa,ac){N.call(this,ab,aa,ac)};n(E.prototype,N.prototype,c.prototype,{load_data:function(ac,aa,ae,af,ab,ad){if(ab>1){return}return N.prototype.load_data.call(this,ac,aa,ae,af,ab,ad)}});var Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};n(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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/>").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new x(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+t+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+t+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-t});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+t});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).bind("click",function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("slider").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var aa=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);var ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={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},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac.track_type==="FeatureTrack"){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa)};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa){b.call(this,ac,ab,aa)};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var ay=aj.content_div.children();var az=false;for(var ax=ay.length-1,aD=0;ax>=aD;ax--){var aw=$(ay[ax]);if(az){aw.remove()}else{if(aw.children().length!==0){az=true}}}}if(aj.track_type=="FeatureTrack"&&aj.mode=="Histogram"){var aC=-1;for(var ax=0;ax<af.length;ax++){var aF=af[ax].max_val;if(aF>aC){aC=aF}}for(var ax=0;ax<af.length;ax++){if(af[ax].max_val!==aC){var aE=af[ax];aE.canvas.remove();aj.delayed_draw(true,am(ak,ae,aE.index),aE.index,aE.resolution,ad,ae,[],{max:aC})}}}if(aj.filters_manager){var av=aj.filters_manager.filters;for(var aB=0;aB<av.length;aB++){av[aB].update_ui_elt()}var aA=false;if(aj.example_feature){for(var aB=0;aB<av.length;aB++){if(av[aB].applies_to(aj.example_feature)){aA=true;break}}}if(aj.filters_available!==aA){aj.filters_available=aA;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,ag,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ad,ag,ae,ah){var ab=this;var ac=this.view.high-this.view.low,af=(ae-this.view.low)*ah;if(this.left_offset){af-=this.left_offset}var aa=ad.canvas;aa.css({position:"absolute",top:0,left:af,height:""});ag.append(aa);ab.max_height=Math.max(ab.max_height,aa.height());ab.content_div.css("height",ab.max_height+"px");ag.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.track_type="LabelTrack";this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.track_type="ReferenceTrack";this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.reference_track=this;this.left_offset=200;this.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:aa.dbkey};this.data_cache=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_cache=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ad,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,aw,aA,aj,ad){var at=this,aC=aA*M*aw,ab=(aA+1)*M*aw,ap=ab-aC,au=Math.ceil(ap*aj),ar=this.mode,aG=25,ae=this.left_offset,ao,af;if(ar==="Auto"){if(an.dataset_type==="summary_tree"){ar=an.dataset_type}else{if(an.extra_info==="no_detail"){ar="no_detail"}else{var aF=an.data;if(this.view.high-this.view.low>F){ar="Squish"}else{ar="Pack"}}}this.update_auto_mode(ar)}if(ar==="summary_tree"||ar==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aC,ab,200);if(an.max){ak.max=an.max}an=ak}var aD=new I.SummaryTreePainter(an,aC,ab,this.prefs);var av=ac.getContext("2d");av.translate(ae,O);aD.draw(av,au,af);return new l(aA,aw,ac,an.max)}var ao,ah=1;if(ar==="no_detail"||ar==="Squish"||ar==="Pack"){ah=this.incremental_slots(aj,an.data,ar);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var ax=0,az=an.data.length;ax<az;ax++){var ag=an.data[ax];var ay=false;var am;for(var aB=0,aE=al.length;aB<aE;aB++){am=al[aB];am.update_attrs(ag);if(!am.keep(ag)){ay=true;break}}if(!ay){ai.push(ag)}}}var aD=new (this.painter)(ai,aC,ab,this.prefs,ar,ad);var af=aD.get_required_height(ah)+A;var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af;var av=ac.getContext("2d");av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.message){av.fillStyle="red";av.textAlign="left";var aq=av.textBaseline;av.textBaseline="top";av.fillRect(ae,0,ac.width-ae,1);av.fillText(an.message,ae,2);av.textBaseline=aq;if(!an.data){return new b(aA,aw,ac,af)}}this.example_feature=(an.data.length?an.data[0]:undefined);av.translate(ae,A);aD.draw(av,au,af,ao);return new L(aA,aw,ac)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_type="VcfTrack";this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Thu May 19 10:07:53 2011 -0400 +++ b/static/scripts/trackster.js Thu May 19 13:47:52 2011 -0400 @@ -977,7 +977,8 @@ // Create and add track. // TODO: add support for other kinds of tool data tracks. if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); + new_track.change_mode(current_track.mode); } this.track.add_track(new_track); new_track.content_div.text("Starting job."); @@ -1704,19 +1705,11 @@ track.mode = init_mode; track.mode_div.text(init_mode); - var change_mode = function(name) { - track.mode_div.text(name); - // TODO: is it necessary to store the mode in two places (.mode and track_config)? - track.mode = name; - track.track_config.values['mode'] = name; - track.tile_cache.clear(); - track.draw(); - }; var mode_mapping = {}; for (var i = 0, len = track.display_modes.length; i < len; i++) { var mode = track.display_modes[i]; mode_mapping[mode] = function(mode) { - return function() { change_mode(mode); }; + return function() { track.change_mode(mode); }; }(mode); } make_popupmenu(track.mode_div, mode_mapping); @@ -1747,6 +1740,18 @@ }; extend(TiledTrack.prototype, Track.prototype, { /** + * Change track's mode. + */ + change_mode: function(name) { + var track = this; + track.mode_div.text(name); + // TODO: is it necessary to store the mode in two places (.mode and track_config)? + track.mode = name; + track.track_config.values['mode'] = name; + track.tile_cache.clear(); + track.draw(); + }, + /** * Make popup menu for track name. */ make_name_popup_menu: function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Add Picard and fastqc tools to Main
by Bitbucket 19 May '11

19 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8c11dd28a3cf/ changeset: r5585:8c11dd28a3cf user: natefoo date: 2011-05-19 16:07:53 summary: Add Picard and fastqc tools to Main affected #: 1 file (836 bytes) --- a/tool_conf.xml.main Wed May 18 16:52:38 2011 -0400 +++ b/tool_conf.xml.main Thu May 19 10:07:53 2011 -0400 @@ -351,6 +351,8 @@ <tool file="fastx_toolkit/fastx_renamer.xml" /><tool file="fastx_toolkit/fastx_reverse_complement.xml" /><tool file="fastx_toolkit/fastx_trimmer.xml" /> + <label text="FASTQ QC" id="fastq_qc" /> + <tool file="rgenetics/rgFastQC.xml" /></section><section name="NGS: Mapping" id="ngs_mapping"><label text="Illumina" id="illumina"/> @@ -394,6 +396,21 @@ <label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> + <section name="NGS: Picard (beta)" id="picard_beta"> + <label text="QC/Metrics for sam/bam" id="qcsambam"/> + <tool file="picard/picard_BamIndexStats.xml" /> + <tool file="picard/rgPicardASMetrics.xml" /> + <tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardLibComplexity.xml" /> + <tool file="picard/rgPicardInsertSize.xml" /> + <tool file="picard/rgPicardHsMetrics.xml" /> + <label text="bam/sam Cleaning" id="picard-clean" /> + <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool file="picard/picard_ReorderSam.xml" /> + <tool file="picard/picard_ReplaceSamHeader.xml" /> + <tool file="picard/rgPicardFixMate.xml" /> + <tool file="picard/rgPicardMarkDups.xml" /> + </section><label text="RGENETICS" id="rgenetics" /><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 18 May '11

18 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/13d9db4d4503/ changeset: r5583:13d9db4d4503 user: jgoecks date: 2011-05-18 22:52:14 summary: Remove obsolete test values for Cufflinks and Cuffdiff tests. affected #: 2 files (121 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.xml Wed May 18 16:48:02 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Wed May 18 16:52:14 2011 -0400 @@ -158,7 +158,6 @@ <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /><param name="fdr" value="0.05" /> - <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /> --- a/tools/ngs_rna/cufflinks_wrapper.xml Wed May 18 16:48:02 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Wed May 18 16:52:14 2011 -0400 @@ -109,7 +109,6 @@ <param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> - <param name="min_map_quality" value="0"/><param name="use_ref" value="No"/><param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/> http://bitbucket.org/galaxy/galaxy-central/changeset/5e72e101e839/ changeset: r5584:5e72e101e839 user: jgoecks date: 2011-05-18 22:52:38 summary: Merge. affected #: 11 files (1.8 KB) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Wed May 18 16:52:38 2011 -0400 @@ -102,23 +102,22 @@ **Picard documentation** -This is a Galaxy interface for the external package Picard-tools_ tool AddOrReplaceReadGroups_. Picard-tools is supported through the SAMTools_ project. +This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_. - .. _AddOrReplaceReadGroups: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadG… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs, outputs, and parameters** -**Outputs** +Either a sam file or a bam file must be supplied. If a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. -The output file is either bam (the default) or sam, according to user selection, and contains the same information as the input file except for the appropraite additional (or modified) read group tags. Bam is recommended since it is smaller. - -**AddOrReplaceReadGroups parameters** +The output file is either bam (the default) or sam, according to user selection, +and contains the same information as the input file except for the appropraite +additional (or modified) read group tags. Bam is recommended since it is smaller. From the Picard documentation. @@ -139,7 +138,17 @@ RGCN=String Read Group sequencing center name; Default value: null (empty) RGDS=String Read Group description Default value: null (empty) -One parameter that Picard's AddOrReplaceReadGroups offers that is automatically set by Galaxy is the SORT_ORDER, which is set to coordinate. +One parameter that Picard's AddOrReplaceReadGroups offers that is automatically +set by Galaxy is the SORT_ORDER, which is set to coordinate. + +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/picard_BamIndexStats.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Wed May 18 16:52:38 2011 -0400 @@ -39,27 +39,35 @@ **Purpose** -Generate Bam Index Stats for a provided bam file +Generate Bam Index Stats for a provided bam file. **Picard documentation** -This is a Galaxy wrapper for BamIndexStats_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_. - .. _BamIndexStats: http://picard.sourceforge.net/command-line-overview.shtml#BamIndexStats - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -The only input is the bam file you wish to obtain statistics for, which is required. Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +The only input is the bam file you wish to obtain statistics for, which is required. +Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. This tool outputs an HTML file that contains links to the actual metrics results, as well as a log file with info on the exact command run. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ------ **Example** --- a/tools/picard/picard_ReorderSam.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Wed May 18 16:52:38 2011 -0400 @@ -106,29 +106,49 @@ **Purpose** -Reorder Sam to match contig ordering in a particular reference file. Note that this is not the same as sorting as done by the SortSam tool, which sorts by either coordinate values or query name. The ordering in ReorderSam is based on exact name matching of contigs. Reads that are mapped to a contig that is not in the new reference file are not included in the output. +Reorder Sam to match contig ordering in a particular reference file. Note that this is +not the same as sorting as done by the SortSam tool, which sorts by either coordinate +values or query name. The ordering in ReorderSam is based on exact name matching of +contigs. Reads that are mapped to a contig that is not in the new reference file are +not included in the output. **Picard documentation** -This is a Galaxy interface for Picard-tools_ tool ReorderSam_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_. - .. _ReorderSam: http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -For the file that needs to be reordered, either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. A reference file is also required, so either a fasta file should be supplied or a built-in reference can be selected. +**Inputs, outputs, and parameters** -**Outputs** +For the file that needs to be reordered, either a sam file or a bam file must be supplied. +If a bam file is used, it must be coordinate-sorted. A reference file is also required, +so either a fasta file should be supplied or a built-in reference can be selected. -The output contains the same reads as the input file but the reads have been rearranged so they appear in the same order as the provided reference file. The tool will output either bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. +The output contains the same reads as the input file but the reads have been rearranged so +they appear in the same order as the provided reference file. The tool will output either +bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. -**ReorderSam parameters** +The only extra parameters that can be set are flags for allowing incomplete dict concordance +and allowing contig length discordance. If incomplete dict concordance is allowed, only a +partial overlap of the bam contigs with the new reference sequence contigs is required. By +default it is off, requiring a corresponding contig in the new reference for each read contig. +If contig length discordance is allowed, contig names that are the same between a read and the +new reference contig are allowed even if they have different lengths. This is usually not a +good idea, unless you know exactly what you're doing. It's off by default. -The only extra parameters that can be set are flags for allowing incomplete dict concordance and allowing contig length discordance. If incomplete dict concordance is allowed, only a partial overlap of the bam contigs with the new reference sequence contigs is required. By default it is off, requiring a corresponding contig in the new reference for each read contig. If contig length discordance is allowed, contig names that are the same between a read and the new reference contig are allowed even if they have different lengths. This is usually not a good idea, unless you know exactly what you're doing. It's off by default. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/picard_ReplaceSamHeader.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Wed May 18 16:52:38 2011 -0400 @@ -61,28 +61,42 @@ **Purpose** -Replace Sam Header with the header from another sam file. The tool does not do any significant validation, so it's up to the user to make sure that the elements in the header are relevant and that the new header has all the required things. +Replace Sam Header with the header from another sam file. The tool does not do any +significant validation, so it's up to the user to make sure that the elements in +the header are relevant and that the new header has all the required things. -Replace the SAMFileHeader in a SAM file with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input files must be the same. +Replace the SAMFileHeader in a SAM file with the given header. Validation is +minimal. It is up to the user to ensure that all the elements referred to in the +SAMRecords are present in the new header. Sort order of the two input files must +be the same. **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool ReplaceSamHeader_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_. - .. _ReplaceSamHeader: http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file is required as the file whose header will be replaced. The header file is also required and can also be either sam or bam (it does not have to be the same type as the other file). In both cases, if a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +Either a sam file or a bam file is required as the file whose header will be replaced. +The header file is also required and can also be either sam or bam (it does not have +to be the same type as the other file). In both cases, if a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. The tool will output either bam (the default) or sam. Bam is recommended since it is smaller. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/rgPicardASMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -76,6 +76,19 @@ </tests><help> +.. class:: infomark + +**Summary** + +This Galaxy tool uses Picard to report high-level measures of alignment based on a provided sam or bam file. + +**Picard documentation** + +This is a Galaxy wrapper for CollectAlignmentSummaryMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- .. class:: infomark @@ -88,23 +101,6 @@ - **Bisulphite data** see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - **Maximum acceptable insertion length** See Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - ------ - -.. class:: infomark - -**Summary** - -This Galaxy tool uses Picard to report measures of alignment. - -**Picard documentation** - -This is a Galaxy wrapper for CollectAlignmentSummaryMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectAlignmentSummaryMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - ----- .. class:: infomark @@ -113,10 +109,6 @@ The Picard documentation (reformatted for Galaxy) says: -**Collect Alignment Summary Metrics** - -Reads a SAM or BAM file and writes a file containing summary alignment metrics. - .. csv-table:: ASMDoc :header-rows: 1 @@ -130,13 +122,7 @@ "IS_BISULFITE_SEQUENCED=Boolean","Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. " "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created." - -AlignmentSummaryMetrics - -High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file -with the extension ".alignment_summary_metrics". - -Output Column Definitions +The output produced by the tool has the following columns: #. CATEGORY: One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregeted for both first and second reads in a pair. #. TOTAL_READS: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters. @@ -158,6 +144,15 @@ #. PCT_CHIMERAS: The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes. #. PCT_ADAPTER: The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -168,9 +163,6 @@ Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam files that Picard will be picky about otherwise. -There is a clean sam tool - but only filters what it ignores. The lenient flag allows reads to be discarded if they're empty or don't map. -This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages. </help></tool> --- a/tools/picard/rgPicardFixMate.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Wed May 18 16:52:38 2011 -0400 @@ -50,6 +50,12 @@ Ensure that all mate-pair information is in sync between each read and it's mate pair. +**Picard documentation** + +This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. class:: warningmark **Useful for paired data only** @@ -59,20 +65,6 @@ the data you choose are valid (paired end) sam or bam data - unless you trust this tool not to harm your data. -**Picard documentation** - -This is a Galaxy wrapper for FixMateInformation_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _FixMateInformation: http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - -**Why you might want to use this tool** - -This tool provides a Galaxy interface to one of the Picard tools. -If you need to repair broken paired read sam/bam files, the Picard tool may help. - ----- .. class:: infomark @@ -100,6 +92,16 @@ "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + + </help></tool> --- a/tools/picard/rgPicardGCBiasMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -74,6 +74,20 @@ .. class:: infomark +**Summary** + +This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. + +**Picard documentation** + +This is a Galaxy wrapper for CollectGcBiasMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark + **Syntax** - **Input** is sam/bam format aligned short read data in your current history @@ -86,23 +100,6 @@ .. class:: infomark -**Summary** - -This Galaxy tool uses Picard to report measures of GC bias. - -**Picard documentation** - -This is a Galaxy wrapper for CollectGcBiasMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectGcBiasMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectGcBiasMetr… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - ------ - -.. class:: infomark - **Inputs, outputs, and parameters** The Picard documentation (reformatted for Galaxy) says: @@ -120,11 +117,7 @@ "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." -GcBiasDetailMetrics - - Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. - -Output Column Definitions +The output produced by the tool has the following columns: #. GC: The G+C content of the reference sequence represented by this bin. Values are from 0% to 100% #. WINDOWS: The number of windows on the reference genome that have this G+C content. @@ -133,6 +126,15 @@ #. NORMALIZED_COVERAGE: The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average). #. ERROR_BAR_WIDTH: The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -143,13 +145,5 @@ MINIMUM_GENOME_FRACTION=0.00001 INPUT=test.bam OUTPUT=picardASMetrics.txt OUTPUT=test.txt CHART_OUTPUT=test.pdf WINDOW_SIZE=100 VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam -files that Picard will be picky about otherwise. -There is a clean sam tool - but only filters what it ignores. The lenient -flag allows reads to be discarded if they're empty or don't map. -This seems an awful strategy but unfortunately may be needed to run an analysis -using badly behaved external packages. - </help></tool> --- a/tools/picard/rgPicardHsMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -114,22 +114,23 @@ #. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X. #. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark - -*Typical tool invocation without Galaxy is on a command line - eg:* +**Typical tool invocation without Galaxy is on a command line - eg:** java -jar /share/shared/galaxy/tool-data/shared/jars/CalculateHsMetrics.jar BAIT_INTERVALS=test.pic TARGET_INTERVALS=test.pic INPUT=test.bam OUTPUT=picardHsMetrics.txt VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it as some of the external packages that -Galaxy relies upon are capable of producing sam/bam -files that Picard will refuse to parse. - -The lenient flag means reads are discarded if empty or off the end of the map - or whatever. Suggestions for -improvement are welcome. - </help></tool> --- a/tools/picard/rgPicardInsertSize.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Wed May 18 16:52:38 2011 -0400 @@ -44,20 +44,18 @@ Reads a SAM or BAM file and describes the distribution of insert size (excluding duplicates) with metrics and a histogram plot. +**Picard documentation** + +This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. class:: warningmark **Useful for paired data only** This tool works for paired data only and can be expected to fail for single end data. -**Picard documentation** - -This is a Galaxy wrapper for CollectInsertSizeMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectInsertSizeMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - ----- .. class:: infomark @@ -79,5 +77,14 @@ "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/rgPicardLibComplexity.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Wed May 18 16:52:38 2011 -0400 @@ -72,26 +72,9 @@ **Picard documentation** -This is a Galaxy wrapper for EstimateLibraryComplexity_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_. - .. _EstimateLibraryComplexity: http://picard.sourceforge.net/command-line-overview.shtml#EstimateLibraryCo… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - -**Why you might want to use this tool** - -This tool provides a Galaxy interface to one of the Picard tools. -If you need to estimate library complexity from sequences, the Picard tool may help. - - -**Note on the Regular Expression** - -(from the Picard docs) -This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. -These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. -The regular expression should contain three capture groups for the three variables, in order. -Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ----- @@ -114,6 +97,26 @@ "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. " +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + +**Note on the Regular Expression** + +(from the Picard docs) +This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. +These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. +The regular expression should contain three capture groups for the three variables, in order. +Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + + </help></tool> --- a/tools/picard/rgPicardMarkDups.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Wed May 18 16:52:38 2011 -0400 @@ -72,11 +72,13 @@ **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool MarkDuplicates, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for MarkDuplicates, a part of the external package Picard-tools_. - .. _MarkDuplicates: http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark **Inputs, outputs, and parameters** @@ -96,6 +98,17 @@ "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. " "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + **Note on the Regular Expression** (from the Picard docs) @@ -109,12 +122,6 @@ remove duplicates option is selected. In some cases you may want to do this, but please only do this if you really understand what you are doing. -**Why you might want to use this tool** - - This tool provides a Galaxy interface to one of the Picard tools. - If you need to estimate library complexity from sequences, the Picard tool may help. - - </help></tool> 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: 2 new changesets
by Bitbucket 18 May '11

18 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0268c14594e0/ changeset: r5581:0268c14594e0 user: kellyv date: 2011-05-18 22:50:37 summary: Further tweaks to Picard help text affected #: 11 files (1.8 KB) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Wed May 18 16:50:37 2011 -0400 @@ -102,23 +102,22 @@ **Picard documentation** -This is a Galaxy interface for the external package Picard-tools_ tool AddOrReplaceReadGroups_. Picard-tools is supported through the SAMTools_ project. +This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_. - .. _AddOrReplaceReadGroups: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadG… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs, outputs, and parameters** -**Outputs** +Either a sam file or a bam file must be supplied. If a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. -The output file is either bam (the default) or sam, according to user selection, and contains the same information as the input file except for the appropraite additional (or modified) read group tags. Bam is recommended since it is smaller. - -**AddOrReplaceReadGroups parameters** +The output file is either bam (the default) or sam, according to user selection, +and contains the same information as the input file except for the appropraite +additional (or modified) read group tags. Bam is recommended since it is smaller. From the Picard documentation. @@ -139,7 +138,17 @@ RGCN=String Read Group sequencing center name; Default value: null (empty) RGDS=String Read Group description Default value: null (empty) -One parameter that Picard's AddOrReplaceReadGroups offers that is automatically set by Galaxy is the SORT_ORDER, which is set to coordinate. +One parameter that Picard's AddOrReplaceReadGroups offers that is automatically +set by Galaxy is the SORT_ORDER, which is set to coordinate. + +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/picard_BamIndexStats.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Wed May 18 16:50:37 2011 -0400 @@ -39,27 +39,35 @@ **Purpose** -Generate Bam Index Stats for a provided bam file +Generate Bam Index Stats for a provided bam file. **Picard documentation** -This is a Galaxy wrapper for BamIndexStats_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_. - .. _BamIndexStats: http://picard.sourceforge.net/command-line-overview.shtml#BamIndexStats - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -The only input is the bam file you wish to obtain statistics for, which is required. Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +The only input is the bam file you wish to obtain statistics for, which is required. +Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. This tool outputs an HTML file that contains links to the actual metrics results, as well as a log file with info on the exact command run. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ------ **Example** --- a/tools/picard/picard_ReorderSam.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Wed May 18 16:50:37 2011 -0400 @@ -106,29 +106,49 @@ **Purpose** -Reorder Sam to match contig ordering in a particular reference file. Note that this is not the same as sorting as done by the SortSam tool, which sorts by either coordinate values or query name. The ordering in ReorderSam is based on exact name matching of contigs. Reads that are mapped to a contig that is not in the new reference file are not included in the output. +Reorder Sam to match contig ordering in a particular reference file. Note that this is +not the same as sorting as done by the SortSam tool, which sorts by either coordinate +values or query name. The ordering in ReorderSam is based on exact name matching of +contigs. Reads that are mapped to a contig that is not in the new reference file are +not included in the output. **Picard documentation** -This is a Galaxy interface for Picard-tools_ tool ReorderSam_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_. - .. _ReorderSam: http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -For the file that needs to be reordered, either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. A reference file is also required, so either a fasta file should be supplied or a built-in reference can be selected. +**Inputs, outputs, and parameters** -**Outputs** +For the file that needs to be reordered, either a sam file or a bam file must be supplied. +If a bam file is used, it must be coordinate-sorted. A reference file is also required, +so either a fasta file should be supplied or a built-in reference can be selected. -The output contains the same reads as the input file but the reads have been rearranged so they appear in the same order as the provided reference file. The tool will output either bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. +The output contains the same reads as the input file but the reads have been rearranged so +they appear in the same order as the provided reference file. The tool will output either +bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. -**ReorderSam parameters** +The only extra parameters that can be set are flags for allowing incomplete dict concordance +and allowing contig length discordance. If incomplete dict concordance is allowed, only a +partial overlap of the bam contigs with the new reference sequence contigs is required. By +default it is off, requiring a corresponding contig in the new reference for each read contig. +If contig length discordance is allowed, contig names that are the same between a read and the +new reference contig are allowed even if they have different lengths. This is usually not a +good idea, unless you know exactly what you're doing. It's off by default. -The only extra parameters that can be set are flags for allowing incomplete dict concordance and allowing contig length discordance. If incomplete dict concordance is allowed, only a partial overlap of the bam contigs with the new reference sequence contigs is required. By default it is off, requiring a corresponding contig in the new reference for each read contig. If contig length discordance is allowed, contig names that are the same between a read and the new reference contig are allowed even if they have different lengths. This is usually not a good idea, unless you know exactly what you're doing. It's off by default. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Wed May 18 16:50:37 2011 -0400 @@ -61,28 +61,42 @@ **Purpose** -Replace Sam Header with the header from another sam file. The tool does not do any significant validation, so it's up to the user to make sure that the elements in the header are relevant and that the new header has all the required things. +Replace Sam Header with the header from another sam file. The tool does not do any +significant validation, so it's up to the user to make sure that the elements in +the header are relevant and that the new header has all the required things. -Replace the SAMFileHeader in a SAM file with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input files must be the same. +Replace the SAMFileHeader in a SAM file with the given header. Validation is +minimal. It is up to the user to ensure that all the elements referred to in the +SAMRecords are present in the new header. Sort order of the two input files must +be the same. **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool ReplaceSamHeader_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_. - .. _ReplaceSamHeader: http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file is required as the file whose header will be replaced. The header file is also required and can also be either sam or bam (it does not have to be the same type as the other file). In both cases, if a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +Either a sam file or a bam file is required as the file whose header will be replaced. +The header file is also required and can also be either sam or bam (it does not have +to be the same type as the other file). In both cases, if a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. The tool will output either bam (the default) or sam. Bam is recommended since it is smaller. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/rgPicardASMetrics.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Wed May 18 16:50:37 2011 -0400 @@ -76,6 +76,19 @@ </tests><help> +.. class:: infomark + +**Summary** + +This Galaxy tool uses Picard to report high-level measures of alignment based on a provided sam or bam file. + +**Picard documentation** + +This is a Galaxy wrapper for CollectAlignmentSummaryMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- .. class:: infomark @@ -88,23 +101,6 @@ - **Bisulphite data** see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - **Maximum acceptable insertion length** See Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - ------ - -.. class:: infomark - -**Summary** - -This Galaxy tool uses Picard to report measures of alignment. - -**Picard documentation** - -This is a Galaxy wrapper for CollectAlignmentSummaryMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectAlignmentSummaryMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - ----- .. class:: infomark @@ -113,10 +109,6 @@ The Picard documentation (reformatted for Galaxy) says: -**Collect Alignment Summary Metrics** - -Reads a SAM or BAM file and writes a file containing summary alignment metrics. - .. csv-table:: ASMDoc :header-rows: 1 @@ -130,13 +122,7 @@ "IS_BISULFITE_SEQUENCED=Boolean","Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. " "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created." - -AlignmentSummaryMetrics - -High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file -with the extension ".alignment_summary_metrics". - -Output Column Definitions +The output produced by the tool has the following columns: #. CATEGORY: One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregeted for both first and second reads in a pair. #. TOTAL_READS: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters. @@ -158,6 +144,15 @@ #. PCT_CHIMERAS: The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes. #. PCT_ADAPTER: The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -168,9 +163,6 @@ Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam files that Picard will be picky about otherwise. -There is a clean sam tool - but only filters what it ignores. The lenient flag allows reads to be discarded if they're empty or don't map. -This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages. </help></tool> --- a/tools/picard/rgPicardFixMate.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Wed May 18 16:50:37 2011 -0400 @@ -50,6 +50,12 @@ Ensure that all mate-pair information is in sync between each read and it's mate pair. +**Picard documentation** + +This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. class:: warningmark **Useful for paired data only** @@ -59,20 +65,6 @@ the data you choose are valid (paired end) sam or bam data - unless you trust this tool not to harm your data. -**Picard documentation** - -This is a Galaxy wrapper for FixMateInformation_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _FixMateInformation: http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - -**Why you might want to use this tool** - -This tool provides a Galaxy interface to one of the Picard tools. -If you need to repair broken paired read sam/bam files, the Picard tool may help. - ----- .. class:: infomark @@ -100,6 +92,16 @@ "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + + </help></tool> --- a/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Wed May 18 16:50:37 2011 -0400 @@ -74,6 +74,20 @@ .. class:: infomark +**Summary** + +This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. + +**Picard documentation** + +This is a Galaxy wrapper for CollectGcBiasMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark + **Syntax** - **Input** is sam/bam format aligned short read data in your current history @@ -86,23 +100,6 @@ .. class:: infomark -**Summary** - -This Galaxy tool uses Picard to report measures of GC bias. - -**Picard documentation** - -This is a Galaxy wrapper for CollectGcBiasMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectGcBiasMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectGcBiasMetr… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - ------ - -.. class:: infomark - **Inputs, outputs, and parameters** The Picard documentation (reformatted for Galaxy) says: @@ -120,11 +117,7 @@ "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." -GcBiasDetailMetrics - - Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. - -Output Column Definitions +The output produced by the tool has the following columns: #. GC: The G+C content of the reference sequence represented by this bin. Values are from 0% to 100% #. WINDOWS: The number of windows on the reference genome that have this G+C content. @@ -133,6 +126,15 @@ #. NORMALIZED_COVERAGE: The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average). #. ERROR_BAR_WIDTH: The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -143,13 +145,5 @@ MINIMUM_GENOME_FRACTION=0.00001 INPUT=test.bam OUTPUT=picardASMetrics.txt OUTPUT=test.txt CHART_OUTPUT=test.pdf WINDOW_SIZE=100 VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam -files that Picard will be picky about otherwise. -There is a clean sam tool - but only filters what it ignores. The lenient -flag allows reads to be discarded if they're empty or don't map. -This seems an awful strategy but unfortunately may be needed to run an analysis -using badly behaved external packages. - </help></tool> --- a/tools/picard/rgPicardHsMetrics.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Wed May 18 16:50:37 2011 -0400 @@ -114,22 +114,23 @@ #. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X. #. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark - -*Typical tool invocation without Galaxy is on a command line - eg:* +**Typical tool invocation without Galaxy is on a command line - eg:** java -jar /share/shared/galaxy/tool-data/shared/jars/CalculateHsMetrics.jar BAIT_INTERVALS=test.pic TARGET_INTERVALS=test.pic INPUT=test.bam OUTPUT=picardHsMetrics.txt VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it as some of the external packages that -Galaxy relies upon are capable of producing sam/bam -files that Picard will refuse to parse. - -The lenient flag means reads are discarded if empty or off the end of the map - or whatever. Suggestions for -improvement are welcome. - </help></tool> --- a/tools/picard/rgPicardInsertSize.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Wed May 18 16:50:37 2011 -0400 @@ -44,20 +44,18 @@ Reads a SAM or BAM file and describes the distribution of insert size (excluding duplicates) with metrics and a histogram plot. +**Picard documentation** + +This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. class:: warningmark **Useful for paired data only** This tool works for paired data only and can be expected to fail for single end data. -**Picard documentation** - -This is a Galaxy wrapper for CollectInsertSizeMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. - - .. _CollectInsertSizeMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - ----- .. class:: infomark @@ -79,5 +77,14 @@ "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/rgPicardLibComplexity.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Wed May 18 16:50:37 2011 -0400 @@ -72,26 +72,9 @@ **Picard documentation** -This is a Galaxy wrapper for EstimateLibraryComplexity_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_. - .. _EstimateLibraryComplexity: http://picard.sourceforge.net/command-line-overview.shtml#EstimateLibraryCo… - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ - - -**Why you might want to use this tool** - -This tool provides a Galaxy interface to one of the Picard tools. -If you need to estimate library complexity from sequences, the Picard tool may help. - - -**Note on the Regular Expression** - -(from the Picard docs) -This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. -These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. -The regular expression should contain three capture groups for the three variables, in order. -Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ----- @@ -114,6 +97,26 @@ "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. " +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + +**Note on the Regular Expression** + +(from the Picard docs) +This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. +These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. +The regular expression should contain three capture groups for the three variables, in order. +Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + + </help></tool> --- a/tools/picard/rgPicardMarkDups.xml Tue May 17 21:31:34 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Wed May 18 16:50:37 2011 -0400 @@ -72,11 +72,13 @@ **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool MarkDuplicates, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for MarkDuplicates, a part of the external package Picard-tools_. - .. _MarkDuplicates: http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark **Inputs, outputs, and parameters** @@ -96,6 +98,17 @@ "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. " "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + **Note on the Regular Expression** (from the Picard docs) @@ -109,12 +122,6 @@ remove duplicates option is selected. In some cases you may want to do this, but please only do this if you really understand what you are doing. -**Why you might want to use this tool** - - This tool provides a Galaxy interface to one of the Picard tools. - If you need to estimate library complexity from sequences, the Picard tool may help. - - </help></tool> http://bitbucket.org/galaxy/galaxy-central/changeset/e1266905ed7b/ changeset: r5582:e1266905ed7b user: kellyv date: 2011-05-18 22:51:51 summary: merge affected #: 3 files (1.3 KB) --- a/lib/galaxy/model/mapping.py Wed May 18 16:50:37 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed May 18 16:51:51 2011 -0400 @@ -1469,7 +1469,12 @@ latest_workflow=relation( Workflow, post_update=True, primaryjoin=( StoredWorkflow.table.c.latest_workflow_id == Workflow.table.c.id ), lazy=False ), - tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), + tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), + owner_tags=relation( StoredWorkflowTagAssociation, + primaryjoin=and_( StoredWorkflow.table.c.id == StoredWorkflowTagAssociation.table.c.stored_workflow_id, + StoredWorkflow.table.c.user_id == StoredWorkflowTagAssociation.table.c.user_id ), + foreign_keys=[StoredWorkflowTagAssociation.table.c.user_id], + order_by=StoredWorkflowTagAssociation.table.c.id ), annotations=relation( StoredWorkflowAnnotationAssociation, order_by=StoredWorkflowAnnotationAssociation.table.c.id, backref="stored_workflows" ), ratings=relation( StoredWorkflowRatingAssociation, order_by=StoredWorkflowRatingAssociation.table.c.id, backref="stored_workflows" ) ) ) --- a/lib/galaxy/web/controllers/workflow.py Wed May 18 16:50:37 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed May 18 16:51:51 2011 -0400 @@ -586,6 +586,7 @@ @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): + # Get workflow to clone. stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user == user: @@ -595,9 +596,24 @@ .filter_by( user=user, stored_workflow=stored ).count() == 0: error( "Workflow is not owned by or shared with current user" ) owner = False + + # Clone. new_stored = model.StoredWorkflow() new_stored.name = "Clone of '%s'" % stored.name new_stored.latest_workflow = stored.latest_workflow + # Clone annotation. + annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored ) + if annotation_obj: + self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation ) + # Clone tags. + for swta in stored.owner_tags: + new_swta = model.StoredWorkflowTagAssociation() + new_swta.tag = swta.tag + new_swta.user = trans.user + new_swta.user_tname = swta.user_tname + new_swta.user_value = swta.user_value + new_swta.value = swta.value + new_stored.tags.append( new_swta ) if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user --- a/templates/tagging_common.mako Wed May 18 16:50:37 2011 -0400 +++ b/templates/tagging_common.mako Wed May 18 16:51:51 2011 -0400 @@ -126,7 +126,7 @@ tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) ) elt_id = int ( floor ( random()*maxint ) ) - # Get list of user's item tags. TODO: this could be moved to a database query for speed purposes. + # Get list of user's item tags. TODO: implement owner_tags for all taggable objects and use here. item_tags = [ tag for tag in tagged_item.tags if ( tag.user == user ) ] %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Clone annotation and tags when cloning workflows.
by Bitbucket 18 May '11

18 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ffba3d4a66d5/ changeset: r5580:ffba3d4a66d5 user: jgoecks date: 2011-05-18 22:48:02 summary: Clone annotation and tags when cloning workflows. affected #: 3 files (1.3 KB) --- a/lib/galaxy/model/mapping.py Tue May 17 21:31:34 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed May 18 16:48:02 2011 -0400 @@ -1469,7 +1469,12 @@ latest_workflow=relation( Workflow, post_update=True, primaryjoin=( StoredWorkflow.table.c.latest_workflow_id == Workflow.table.c.id ), lazy=False ), - tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), + tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), + owner_tags=relation( StoredWorkflowTagAssociation, + primaryjoin=and_( StoredWorkflow.table.c.id == StoredWorkflowTagAssociation.table.c.stored_workflow_id, + StoredWorkflow.table.c.user_id == StoredWorkflowTagAssociation.table.c.user_id ), + foreign_keys=[StoredWorkflowTagAssociation.table.c.user_id], + order_by=StoredWorkflowTagAssociation.table.c.id ), annotations=relation( StoredWorkflowAnnotationAssociation, order_by=StoredWorkflowAnnotationAssociation.table.c.id, backref="stored_workflows" ), ratings=relation( StoredWorkflowRatingAssociation, order_by=StoredWorkflowRatingAssociation.table.c.id, backref="stored_workflows" ) ) ) --- a/lib/galaxy/web/controllers/workflow.py Tue May 17 21:31:34 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed May 18 16:48:02 2011 -0400 @@ -586,6 +586,7 @@ @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): + # Get workflow to clone. stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user == user: @@ -595,9 +596,24 @@ .filter_by( user=user, stored_workflow=stored ).count() == 0: error( "Workflow is not owned by or shared with current user" ) owner = False + + # Clone. new_stored = model.StoredWorkflow() new_stored.name = "Clone of '%s'" % stored.name new_stored.latest_workflow = stored.latest_workflow + # Clone annotation. + annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored ) + if annotation_obj: + self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation ) + # Clone tags. + for swta in stored.owner_tags: + new_swta = model.StoredWorkflowTagAssociation() + new_swta.tag = swta.tag + new_swta.user = trans.user + new_swta.user_tname = swta.user_tname + new_swta.user_value = swta.user_value + new_swta.value = swta.value + new_stored.tags.append( new_swta ) if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user --- a/templates/tagging_common.mako Tue May 17 21:31:34 2011 -0400 +++ b/templates/tagging_common.mako Wed May 18 16:48:02 2011 -0400 @@ -126,7 +126,7 @@ tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) ) elt_id = int ( floor ( random()*maxint ) ) - # Get list of user's item tags. TODO: this could be moved to a database query for speed purposes. + # Get list of user's item tags. TODO: implement owner_tags for all taggable objects and use here. item_tags = [ tag for tag in tagged_item.tags if ( tag.user == user ) ] %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kellyv: Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible
by Bitbucket 17 May '11

17 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bee3d356198a/ changeset: r5579:bee3d356198a user: kellyv date: 2011-05-18 03:31:34 summary: Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible affected #: 12 files (2.2 KB) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 21:31:34 2011 -0400 @@ -98,12 +98,13 @@ **Purpose** -Add or Replace Read Groups in an input bam or sam file +Add or Replace Read Groups in an input bam or sam file. **Picard documentation** -This is a Galaxy interface for the Picard-tools_ tool AddOrReplaceReadGroups. Picard-tools is supported through the SAMTools_ project. +This is a Galaxy interface for the external package Picard-tools_ tool AddOrReplaceReadGroups_. Picard-tools is supported through the SAMTools_ project. + .. _AddOrReplaceReadGroups: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadG… .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ @@ -129,12 +130,12 @@ RGPL=String Read Group platform (e.g. illumina, solid) RGPU=String Read Group platform unit (eg. run barcode) RGSM=String Read Group sample name + RGID=String Read Group ID; Default value: null (empty) AddOrReplaceReadGroups OPTIONAL parameters:: Option (Type) Description - RGID=String Read Group ID; Default value: null (empty) RGCN=String Read Group sequencing center name; Default value: null (empty) RGDS=String Read Group description Default value: null (empty) --- a/tools/picard/picard_BamIndexStats.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Tue May 17 21:31:34 2011 -0400 @@ -43,8 +43,9 @@ **Picard documentation** -This is a Galaxy wrapper for BamIndexStats, a part of Picard-tools_, which is closely related to SAMTools_. +This is a Galaxy wrapper for BamIndexStats_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + .. _BamIndexStats: http://picard.sourceforge.net/command-line-overview.shtml#BamIndexStats .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ @@ -56,7 +57,8 @@ **Outputs** -The output from this tool is a simple text file. +This tool outputs an HTML file that contains links to the actual metrics results, as well +as a log file with info on the exact command run. ------ @@ -83,13 +85,13 @@ read7 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 read8 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 -The following file will be produced:: +The following metrics file will be produced:: - chr1 length= 101 Aligned= 0 Unaligned= 0 - chr7 length= 404 Aligned= 7 Unaligned= 0 - chr8 length= 202 Aligned= 0 Unaligned= 0 - chr10 length= 303 Aligned= 0 Unaligned= 0 - chr14 length= 505 Aligned= 0 Unaligned= 0 + chr1 length= 101 Aligned= 0 Unaligned= 0 + chr7 length= 404 Aligned= 7 Unaligned= 0 + chr8 length= 202 Aligned= 0 Unaligned= 0 + chr10 length= 303 Aligned= 0 Unaligned= 0 + chr14 length= 505 Aligned= 0 Unaligned= 0 NoCoordinateCount= 1 </help> --- a/tools/picard/picard_ReorderSam.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Tue May 17 21:31:34 2011 -0400 @@ -110,8 +110,9 @@ **Picard documentation** -This is a Galaxy interface for Picard-tools_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. +This is a Galaxy interface for Picard-tools_ tool ReorderSam_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + .. _ReorderSam: http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ --- a/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 21:31:34 2011 -0400 @@ -67,8 +67,9 @@ **Picard documentation** -This is a Galaxy interface to the Picard-tools_'s ReplaceSamHeader tools, which is supported by SAMTools_. +This is a Galaxy interface to the external package Picard-tools_ tool ReplaceSamHeader_, which is supported by the SAMTools_ project. + .. _ReplaceSamHeader: http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ --- a/tools/picard/rgPicardASMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -95,30 +95,29 @@ **Summary** -This Galaxy tool uses Picard to report measures of alignment -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. +This Galaxy tool uses Picard to report measures of alignment. -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… -Some of that material is consolidated below from the Picard documentation +**Picard documentation** + +This is a Galaxy wrapper for CollectAlignmentSummaryMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectAlignmentSummaryMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ ----- .. class:: infomark -**Picard Documentation** +**Inputs, outputs, and parameters** The Picard documentation (reformatted for Galaxy) says: -***Collect Alignment Summary Metrics*** +**Collect Alignment Summary Metrics** - Reads a SAM or BAM file and writes a file containing summary alignment metrics. +Reads a SAM or BAM file and writes a file containing summary alignment metrics. .. csv-table:: ASMDoc - :header-rows: 1 Option,Description @@ -173,16 +172,6 @@ There is a clean sam tool - but only filters what it ignores. The lenient flag allows reads to be discarded if they're empty or don't map. This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages. ------ - -.. class:: infomark - -**Attribution** - -Picard and Samtools go together. They are external to and completely independent of Galaxy. We acknowledge that all credit for -their methods and contribution are due to them. - - </help></tool> --- a/tools/picard/rgPicardFixMate.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Tue May 17 21:31:34 2011 -0400 @@ -46,6 +46,12 @@ .. class:: infomark +**Purpose** + +Ensure that all mate-pair information is in sync between each read and it's mate pair. + +.. class:: warningmark + **Useful for paired data only** Likely won't do anything helpful for single end sequence data @@ -53,9 +59,14 @@ the data you choose are valid (paired end) sam or bam data - unless you trust this tool not to harm your data. -**Purpose** +**Picard documentation** -Ensure that all mate-pair information is in sync between each read and it's mate pair. +This is a Galaxy wrapper for FixMateInformation_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _FixMateInformation: http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + **Why you might want to use this tool** @@ -77,7 +88,7 @@ .. class:: infomark -**From the Picard documentation** +**Inputs, outputs, and parameters** .. csv-table:: Fixmate @@ -89,20 +100,6 @@ "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml - </help></tool> --- a/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -89,35 +89,36 @@ **Summary** This Galaxy tool uses Picard to report measures of GC bias. -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… +**Picard documentation** + +This is a Galaxy wrapper for CollectGcBiasMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectGcBiasMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectGcBiasMetr… + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + ----- .. class:: infomark -**Picard Documentation** +**Inputs, outputs, and parameters** The Picard documentation (reformatted for Galaxy) says: .. csv-table:: GC Bias Doc :header-rows: 1 - Option,Description - "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required." - "INPUT=File","The BAM or SAM file containing aligned reads. Required." - "OUTPUT=File","The text file to write the metrics table to. Required." - "CHART_OUTPUT=File","The PDF file to render the chart to. Required." - "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null." - "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100." - "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." - "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." - + Option,Description + "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required." + "INPUT=File","The BAM or SAM file containing aligned reads. Required." + "OUTPUT=File","The text file to write the metrics table to. Required." + "CHART_OUTPUT=File","The PDF file to render the chart to. Required." + "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null." + "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100." + "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." + "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." GcBiasDetailMetrics @@ -136,7 +137,6 @@ .. class:: infomark - **Typical tool invocation without Galaxy is on a command line - eg:** java -jar /share/shared/galaxy/tool-data/shared/jars/CollectGcBiasMetrics.jar REFERENCE_SEQUENCE="hg18.fasta" @@ -151,15 +151,5 @@ This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages. ------ - -.. class:: infomark - -**Attributions** - -Picard and Samtools go together. -They are external to and completely independent of Galaxy. We acknowledge that all credit for -their methods and contribution are due to them. - </help></tool> --- a/tools/picard/rgPicardHsMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -40,21 +40,27 @@ **Summary** -This tool provides a Galaxy interface to one of the Picard tools freely -available at http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics +Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file. + +**Picard documentation** + +This is a Galaxy wrapper for CalculateHsMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CalculateHsMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + ----- .. class:: infomark -**Picard Documentation** +**Inputs, outputs, and parameters** -Picard documentation says: - +Picard documentation says (reformatted for Galaxy): Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file. - .. csv-table:: HsDoc :header-rows: 1 @@ -125,20 +131,5 @@ The lenient flag means reads are discarded if empty or off the end of the map - or whatever. Suggestions for improvement are welcome. ------ - -.. class:: infomark - -**Attribution** - -This tool takes interval files in the usual Galaxy interval (bed) format as bait and target sequences rather than -the special format Picard requires - the tool provides reliable reformatting for Picard. - -Picard is a project associated with the SamTools project. -This Galaxy tool uses part of Picard to report measures of hybridization selection in your -aligned short read sequence data. Sequence data must be chosen from the sam/bam format files in your current history. -Target and bait files must be selected from the UCSC BED format in your current history. - - </help></tool> --- a/tools/picard/rgPicardInsertSize.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Tue May 17 21:31:34 2011 -0400 @@ -41,16 +41,30 @@ **Purpose** -This tool works for PAIRED DATA ONLY and can be expected to fail for single end data. +Reads a SAM or BAM file and describes the distribution +of insert size (excluding duplicates) with metrics and a histogram plot. -Reads a SAM or BAM file and describes the distribution -of insert size (excluding duplicates). Generates a histogram plot. +.. class:: warningmark + +**Useful for paired data only** + +This tool works for paired data only and can be expected to fail for single end data. + +**Picard documentation** + +This is a Galaxy wrapper for CollectInsertSizeMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectInsertSizeMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ ----- .. class:: infomark -**From the Picard documentation** +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy): .. csv-table:: Insert size metrics docs :header-rows: 1 @@ -65,21 +79,5 @@ "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." - ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml - - </help></tool> --- a/tools/picard/rgPicardLibComplexity.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Tue May 17 21:31:34 2011 -0400 @@ -55,42 +55,51 @@ **Purpose** - EstimateLibraryComplexity - Attempts to estimate library complexity from sequence alone. - Does so by sorting all reads by the first N bases (5 by default) of each read and then - comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be - duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default). +Attempts to estimate library complexity from sequence alone. +Does so by sorting all reads by the first N bases (5 by default) of each read and then +comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be +duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default). - Reads of poor quality are filtered out so as to provide a more accurate estimate. - The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than - MIN_MEAN_QUALITY across either the first or second read. +Reads of poor quality are filtered out so as to provide a more accurate estimate. +The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than +MIN_MEAN_QUALITY across either the first or second read. - The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the - calculation of library size. Also, since there is no alignment to screen out technical reads one - further filter is applied on the data. After examining all reads a histogram is built of - [#reads in duplicate set -> #of duplicate sets]; - all bins that contain exactly one duplicate set are then removed from the histogram as outliers before library size is estimated. +The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the +calculation of library size. Also, since there is no alignment to screen out technical reads one +further filter is applied on the data. After examining all reads a histogram is built of +[#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are +then removed from the histogram as outliers before library size is estimated. + +**Picard documentation** + +This is a Galaxy wrapper for EstimateLibraryComplexity_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _EstimateLibraryComplexity: http://picard.sourceforge.net/command-line-overview.shtml#EstimateLibraryCo… + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + **Why you might want to use this tool** - This tool provides a Galaxy interface to one of the Picard tools. - If you need to estimate library complexity from sequences, the Picard tool may help. +This tool provides a Galaxy interface to one of the Picard tools. +If you need to estimate library complexity from sequences, the Picard tool may help. **Note on the Regular Expression** - (from the Picard docs) - This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. - These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. - The regular expression should contain three capture groups for the three variables, in order. - Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. - +(from the Picard docs) +This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. +These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. +The regular expression should contain three capture groups for the three variables, in order. +Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. ----- .. class:: infomark -**From the Picard documentation** +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy): .. csv-table:: Estimate complexity docs :header-rows: 1 @@ -105,21 +114,6 @@ "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. " - ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -Please help us by completing the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… - </help></tool> --- a/tools/picard/rgPicardMarkDups.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Tue May 17 21:31:34 2011 -0400 @@ -56,7 +56,7 @@ <param name="remDups" value="true" /><param name="assumeSorted" value="true" /><param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> - <param name="optDupeDist" value="100" /> + <param name="optDupeDist" value="100" /><output name="out_file" file="picard_output_markdups_remdupes.bam" ftype="bam" compare="diff" /><output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" /></test> @@ -68,9 +68,19 @@ **Purpose** -MarkDuplicates +Marks all duplicate reads in a provided sam or bam file and either removes them or flags them. -**From the Picard documentation** +**Picard documentation** + +This is a Galaxy interface to the external package Picard-tools_ tool MarkDuplicates, which is supported by the SAMTools_ project. + + .. _MarkDuplicates: http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy): .. csv-table:: Mark Duplicates docs :header-rows: 1 @@ -86,7 +96,6 @@ "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. " "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" - **Note on the Regular Expression** (from the Picard docs) @@ -105,19 +114,6 @@ This tool provides a Galaxy interface to one of the Picard tools. If you need to estimate library complexity from sequences, the Picard tool may help. ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… </help></tool> --- a/tools/rgenetics/rgFastQC.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Tue May 17 21:31:34 2011 -0400 @@ -6,7 +6,9 @@ -c "$contaminants" #end if </command> -<requirements><requirement type="package">FastQC</requirement></requirements> + <requirements> + <requirement type="package">FastQC</requirement> + </requirements><inputs><param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /><param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80" /> @@ -30,35 +32,57 @@ **Purpose** -FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. -It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of +FastQC aims to provide a simple way to do some quality control checks on raw +sequence data coming from high throughput sequencing pipelines. +It provides a modular set of analyses which you can use to give a quick +impression of whether your data has any problems of which you should be aware before doing any further analysis. -The main functions of FastQC are +The main functions of FastQC are: -Import of data from BAM, SAM or FastQ files (any variant) -Providing a quick overview to tell you in which areas there may be problems -Summary graphs and tables to quickly assess your data -Export of results to an HTML based permanent report -Offline operation to allow automated generation of reports without running the interactive application +- Import of data from BAM, SAM or FastQ files (any variant) +- Providing a quick overview to tell you in which areas there may be problems +- Summary graphs and tables to quickly assess your data +- Export of results to an HTML based permanent report +- Offline operation to allow automated generation of reports without running the interactive application + +**FastQC documentation** + +This is a Galaxy interface to the external package FastQC_. +Specific documentation on FastQC can be found on that site. +FastQC incorporates the Picard-tools_ libraries for sam/bam processing. + + .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + +The contaminants file parameter was borrowed from the independently developed +fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. ----- .. class:: infomark -**Attribution** +**Inputs and outputs** -FastQC comes from http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ -Please see that site for all documentation - this is just a Galaxy wrapper. -This tool wraps the fastqc package to report some QC metrics on fastq, groomed fastq (fastqsanger) in Galaxy +This wrapper will accept any fastq file as well as sam or bam as the primary file to check. +It will also take an optional file containing a list of contaminants information, in the form of +a tab-delimited file with 2 columns, name and sequence. -This Galaxy tool wrapper is part of the rgenetics toolkit. +The tool produces a single HTML output file that contains all of the results, including the following: -Contaminants file parameter borrowed from the independently -developed fastqcwrapper_ contributed to the galaxy community tool shed -by j johnson +- Basic Statistics +- Per base sequence quality +- Per sequence quality scores +- Per base sequence content +- Per base GC content +- Per sequence GC content +- Per base N content +- Sequence Length Distribution +- Sequence Duplication Levels +- Overrepresented sequences +- Kmer Content -.. _fastqcwrapper: http%3A//community.g2.bx.psu.edu/tool/browse_tools%3F%26webapp%3Dcommunity%26operation%3Dview_tool%26id%3D256f9f17b153ce60 +All except Basic Statistics and Overrepresented sequences are plots. </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Fix data.py typo. Fixes #543
by Bitbucket 17 May '11

17 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d2ba41bec611/ changeset: r5578:d2ba41bec611 user: kanwei date: 2011-05-18 00:41:12 summary: Fix data.py typo. Fixes #543 affected #: 1 file (1 byte) --- a/lib/galaxy/datatypes/data.py Tue May 17 13:14:15 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Tue May 17 18:41:12 2011 -0400 @@ -84,7 +84,7 @@ def get_raw_data( self, dataset ): """Returns the full data. To stream it open the file_name and read/write as needed""" try: - return file(datset.file_name, 'rb').read(-1) + return file(dataset.file_name, 'rb').read(-1) except OSError, e: log.exception('%s reading a file that does not exist %s' % (self.__class__.__name__, dataset.file_name)) return '' 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: fubar: grr - more vanity attribution removed
by Bitbucket 17 May '11

17 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/59a2bee2b725/ changeset: r5577:59a2bee2b725 user: fubar date: 2011-05-17 19:14:15 summary: grr - more vanity attribution removed affected #: 1 file (298 bytes) --- a/tools/picard/rgPicardFixMate.xml Tue May 17 13:04:35 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Tue May 17 13:14:15 2011 -0400 @@ -103,13 +103,6 @@ All the Picard tools are freely available and are documented at http://picard.sourceforge.net/command-line-overview.shtml -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -Code cleaned up and the ugliest hacks repaired by Raphael Lullis. -Kelly Vincent wrote the first version of picard_wrapper.py that now incorporates that code. - -It takes a village of programmers to wrap a picard tool - - </help></tool> 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: 2 new changesets
by Bitbucket 17 May '11

17 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/eec910f20a4e/ changeset: r5575:eec910f20a4e user: fubar date: 2011-05-17 18:52:24 summary: separated ngs picard tools and removed fastqc wrapper lgpl annotation affected #: 2 files (192 bytes) --- a/tool_conf.xml.sample Tue May 17 12:14:32 2011 -0400 +++ b/tool_conf.xml.sample Tue May 17 12:52:24 2011 -0400 @@ -242,19 +242,6 @@ <section name="NGS: QC and manipulation" id="NGS_QC"><label text="FastQC: fastq/sam/bam" id="fastqcsambam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="QC/Metrics for sam/bam" id="qcsambam"/> - <tool file="picard/picard_BamIndexStats.xml" /> - <tool file="picard/rgPicardASMetrics.xml" /> - <tool file="picard/rgPicardGCBiasMetrics.xml" /> - <tool file="picard/rgPicardLibComplexity.xml" /> - <tool file="picard/rgPicardInsertSize.xml" /> - <tool file="picard/rgPicardHsMetrics.xml" /> - <label text="bam/sam Cleaning" id="picard-tools" /> - <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> - <tool file="picard/picard_ReorderSam.xml" /> - <tool file="picard/picard_ReplaceSamHeader.xml" /> - <tool file="picard/rgPicardFixMate.xml" /> - <tool file="picard/rgPicardMarkDups.xml" /><label text="Illumina fastq" id="illumina" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /> @@ -293,6 +280,21 @@ <tool file="fastx_toolkit/fastx_reverse_complement.xml" /><tool file="fastx_toolkit/fastx_trimmer.xml" /></section> + <section name="NGS: Picard (beta)" id="picard_beta"> + <label text="QC/Metrics for sam/bam" id="qcsambam"/> + <tool file="picard/picard_BamIndexStats.xml" /> + <tool file="picard/rgPicardASMetrics.xml" /> + <tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardLibComplexity.xml" /> + <tool file="picard/rgPicardInsertSize.xml" /> + <tool file="picard/rgPicardHsMetrics.xml" /> + <label text="bam/sam Cleaning" id="picard-clean" /> + <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool file="picard/picard_ReorderSam.xml" /> + <tool file="picard/picard_ReplaceSamHeader.xml" /> + <tool file="picard/rgPicardFixMate.xml" /> + <tool file="picard/rgPicardMarkDups.xml" /> + </section><!-- Keep this section commented until it includes tools that will be hosted on test/main. The velvet wrappers have been --- a/tools/rgenetics/rgFastQC.xml Tue May 17 12:14:32 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Tue May 17 12:52:24 2011 -0400 @@ -55,15 +55,10 @@ This Galaxy tool wrapper is part of the rgenetics toolkit. Contaminants file parameter borrowed from the independently -developed fastqcwrapper contributed to the galaxy community tool shed +developed fastqcwrapper_ contributed to the galaxy community tool shed by j johnson -copyright Ross Lazarus at g mail dot com 2011 -Licensed under the LGPL_ - .. _fastqcwrapper: http%3A//community.g2.bx.psu.edu/tool/browse_tools%3F%26webapp%3Dcommunity%26operation%3Dview_tool%26id%3D256f9f17b153ce60 -.. _LGPL: http://www.gnu.org/copyleft/lesser.html - </help></tool> http://bitbucket.org/galaxy/galaxy-central/changeset/fa0480c6a01d/ changeset: r5576:fa0480c6a01d user: fubar date: 2011-05-17 19:04:35 summary: cleaned up picard tool names - own section so (picard) was redundant affected #: 12 files (349 bytes) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Add or Replace Groups:" id="picard_ARRG" version="0.2.0"> +<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input="$inputFile" --- a/tools/picard/picard_BamIndexStats.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="BAM Index Statistics:" id="picard_BamIndexStats" version="0.2.0"> +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input "$input_file" --- a/tools/picard/picard_MarkDuplicates.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_MarkDuplicates.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Mark Duplicates:" id="picard_MarkDuplicates" version="0.01"> - <description>(Picard)</description> +<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01"><command interpreter="python"> picard_wrapper.py --input="$input_file" --- a/tools/picard/picard_ReorderSam.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Reorder SAM:" id="picard_ReorderSam" version="0.3.0"> +<tool name="Reorder SAM" id="picard_ReorderSam" version="0.3.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input=$inputFile --- a/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Replace Sam Header:" id="picard_ReplaceSamHeader" version="0.2.0"> +<tool name="Replace Sam Header" id="picard_ReplaceSamHeader" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input "$inputFile" --- a/tools/picard/rgPicardASMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Sam/bam Alignment Summary Metrics:" id="PicardASMetrics" version="0.03"> - <description>(Picard)</description> +<tool name="Sam/bam Alignment Summary Metrics" id="PicardASMetrics" version="0.03"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --- a/tools/picard/rgPicardFixMate.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Paired Read Mate Fixer:" id="rgPicFixMate" version="0.2.0"> +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0"><description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" --- a/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Sam/bam GC Bias Metrics:" id="PicardGCBiasMetrics" version="0.01"> - <description>(Picard)</description> +<tool name="Sam/bam GC Bias Metrics" id="PicardGCBiasMetrics" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" --- a/tools/picard/rgPicardHsMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Sam/bam Hybrid Selection Metrics:" id="PicardHsMetrics" version="0.01"> +<tool name="Sam/bam Hybrid Selection Metrics" id="PicardHsMetrics" version="0.01"><description>For (eg exome) targeted data</description><command interpreter="python"> --- a/tools/picard/rgPicardInsertSize.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Insertion size metrics:" id="PicardInsertSize" version="0.3.0"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> --- a/tools/picard/rgPicardLibComplexity.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Estimate Library Complexity:" id="rgEstLibComp" version="0.01"> - <description>(Picard)</description> +<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" --- a/tools/picard/rgPicardMarkDups.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Mark Duplicates:" id="rgPicardMarkDups" version="0.01"> - <description>(Picard)</description> +<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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