February 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3441: Fix workflow bug where "Layout" changes would ...
by Greg Von Kuster 25 Feb '10

25 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/25015efefdd9 changeset: 3441:25015efefdd9 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Feb 24 18:55:30 2010 -0500 description: Fix workflow bug where "Layout" changes would not be saved, and "Save and Close" did not save diffstat: static/scripts/galaxy.workflow_editor.canvas.js | 1 + static/scripts/packed/galaxy.workflow_editor.canvas.js | 2 +- templates/workflow/editor.mako | 31 ++++++++--------- 3 files changed, 17 insertions(+), 17 deletions(-) diffs (111 lines): diff -r 674aaee19991 -r 25015efefdd9 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Feb 24 16:50:06 2010 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Feb 24 18:55:30 2010 -0500 @@ -476,6 +476,7 @@ }, layout : function () { this.check_changes_in_active_form(); + this.has_changes = true; // Prepare predecessor / successor tracking var n_pred = {}; var successors = {}; diff -r 674aaee19991 -r 25015efefdd9 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Feb 24 16:50:06 2010 -0500 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Feb 24 18:55:30 2010 -0500 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a! ){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*! f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canv as.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callou! t'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProx! y).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dr agProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=! g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j)! )});workflow.node_changed(this)},update_field_data:function(f){var c=$ (this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='! color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.t! ool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.e lement).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_cha! nges_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(! d[p].element).position().top-$(d[o].element).position().top});var m=0; var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).posi! tion();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}! ));i.appendTo("#canvas-container");var d=$("#canvas-container").positi on();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clear! Timeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min! (f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.m in(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_vi! ewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a! ){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*! f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canv as.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callou! t'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProx! y).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dr agProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=! g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j)! )});workflow.node_changed(this)},update_field_data:function(f){var c=$ (this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='! color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.t! ool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.e lement).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_cha! nges_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(f! unction(p,o){return $(d[p].element).position().top-$(d[o].element).pos ition().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(functio! n(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../ima! ges/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#can vas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{te! st:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=fu! nction(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b. cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",fun! ction(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r 674aaee19991 -r 25015efefdd9 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Feb 24 16:50:06 2010 -0500 +++ b/templates/workflow/editor.mako Wed Feb 24 18:55:30 2010 -0500 @@ -163,7 +163,11 @@ } // Show viewport on load unless pref says it's off - $.jStore.store("overview-off") ? hide_overview() : show_overview() + if ($.jStore.store("overview-off")) { + hide_overview(); + } else { + show_overview(); + } }); }); @@ -220,16 +224,15 @@ }); // Rename async. - async_save_text("workflow-name", "workflow-name", "${h.url_for( action="rename_async", id=trans.security.encode_id(stored.id) )}", "new_name"); + async_save_text("workflow-name", "workflow-name", "${h.url_for( action='rename_async', id=trans.security.encode_id(stored.id) )}", "new_name"); // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging. - $('#workflow-tag').click( function() - { + $('#workflow-tag').click( function() { $('.tag-area').click(); return false; }); // Annotate async. - async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( action="annotate_async", id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4); + async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( action='annotate_async', id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4); }); // Global state for the whole workflow @@ -241,7 +244,7 @@ } function scroll_to_nodes() { - var cv = $("#canvas-vieport"); + var cv = $("#canvas-viewport"); var cc = $("#canvas-container") var top, left; if ( cc.width() < cv.width() ) { @@ -352,8 +355,7 @@ // Add metadata form to tool. - if ( node ) - { + if (node) { var metadata_div = $( "<p><div class='metadataForm'> \ <div class='metadataFormTitle'>Edit Step Attributes</div> \ @@ -408,7 +410,7 @@ } return; } - var savefn = function() { + var savefn = function(callback) { $.ajax( { url: "${h.url_for( action='save_workflow' )}", type: "POST", @@ -433,12 +435,12 @@ workflow.name = data.name; workflow.has_changes = false; workflow.stored = true; - if ( success_callback ) { - success_callback(); - } if ( data.errors ) { show_modal( "Saving workflow", body, { "Ok" : hide_modal } ); } else { + if (callback) { + callback(); + } hide_modal(); } } @@ -455,10 +457,7 @@ active_ajax_call = false; }); } else { - savefn(); - } - if ( success_callback ) { - success_callback(); + savefn(success_callback); } }

1 0

[hg] galaxy 3439: Update test framework to allow not setting a v...
by Greg Von Kuster 25 Feb '10

25 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/46849d69d7e6 changeset: 3439:46849d69d7e6 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Feb 24 16:48:22 2010 -0500 description: Update test framework to allow not setting a value for optional DataToolParameter inputs. diffstat: lib/galaxy/tools/test.py | 21 +++++++++++++++++---- 1 files changed, 17 insertions(+), 4 deletions(-) diffs (50 lines): diff -r 841037edd8a0 -r 46849d69d7e6 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Wed Feb 24 15:54:52 2010 -0500 +++ b/lib/galaxy/tools/test.py Wed Feb 24 16:48:22 2010 -0500 @@ -4,6 +4,9 @@ from parameters import basic from parameters import grouping from elementtree.ElementTree import XML +import logging + +log = logging.getLogger( __name__ ) class ToolTestBuilder( object ): """ @@ -27,8 +30,12 @@ if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - self.required_files.append( ( value, extra ) ) - except: pass + if value is None: + assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name + else: + self.required_files.append( ( value, extra ) ) + except Exception, e: + log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) def add_output( self, name, file, sort ): self.outputs.append( ( name, file, sort ) ) @@ -39,7 +46,10 @@ for case in grouping_value.cases: for case_input_name, case_input_value in case.inputs.items(): if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - self.required_files.append( ( value, extra ) ) + if value is None: + assert case_input_value.optional, '%s is not optional. You must provide a valid filename.' % name + else: + self.required_files.append( ( value, extra ) ) return True elif isinstance( case_input_value, grouping.Conditional ): self.__expand_grouping_for_data_input(name, value, extra, case_input_name, case_input_value) @@ -51,5 +61,8 @@ # one used ). for input_name, input_value in grouping_value.inputs.items(): if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - self.required_files.append( ( value, extra ) ) + if value is None: + assert input_value.optional, '%s is not optional. You must provide a valid filename.' % name + else: + self.required_files.append( ( value, extra ) ) return True

1 0

[hg] galaxy 3438: Fix for set metadata tests when setting metada...
by Greg Von Kuster 25 Feb '10

25 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/841037edd8a0 changeset: 3438:841037edd8a0 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Feb 24 15:54:52 2010 -0500 description: Fix for set metadata tests when setting metadata externally diffstat: scripts/functional_tests.py | 5 +++-- test/base/twilltestcase.py | 7 ++++++- 2 files changed, 9 insertions(+), 3 deletions(-) diffs (35 lines): diff -r aece26463c9d -r 841037edd8a0 scripts/functional_tests.py --- a/scripts/functional_tests.py Wed Feb 24 11:57:35 2010 -0500 +++ b/scripts/functional_tests.py Wed Feb 24 15:54:52 2010 -0500 @@ -109,11 +109,12 @@ database_connection = os.environ['GALAXY_TEST_DBURI'] else: database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) + kwargs = {} + for dir in file_path, new_file_path: try: - os.makedirs( file_path ) + os.makedirs( dir ) except OSError: pass - kwargs = {} print "Database connection:", database_connection diff -r aece26463c9d -r 841037edd8a0 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Feb 24 11:57:35 2010 -0500 +++ b/test/base/twilltestcase.py Wed Feb 24 15:54:52 2010 -0500 @@ -475,7 +475,12 @@ self.check_page_for_string( 'This will inspect the dataset and attempt' ) tc.fv( 'auto_detect', 'id', hda_id ) tc.submit( 'detect' ) - self.check_page_for_string( 'Attributes updated' ) + try: + self.check_page_for_string( 'Attributes have been queued to be updated' ) + self.wait() + except AssertionError: + self.check_page_for_string( 'Attributes updated' ) + #self.check_page_for_string( 'Attributes updated' ) self.home() def convert_format( self, hda_id, target_type ): """Convert format of history_dataset_association"""

1 0

[hg] galaxy 3437: Move FASTA classes in galaxy_utils from fastq....
by Greg Von Kuster 25 Feb '10

25 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/aece26463c9d changeset: 3437:aece26463c9d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Feb 24 11:57:35 2010 -0500 description: Move FASTA classes in galaxy_utils from fastq.py to fasta.py. diffstat: lib/galaxy_utils/sequence/fasta.py | 108 +++++++++++++++++++++++++++++++++++++ lib/galaxy_utils/sequence/fastq.py | 107 ------------------------------------ tools/fastq/fastq_combiner.py | 3 +- tools/fastq/fastq_to_fasta.py | 3 +- 4 files changed, 112 insertions(+), 109 deletions(-) diffs (260 lines): diff -r 66ba0f2d6d32 -r aece26463c9d lib/galaxy_utils/sequence/fasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy_utils/sequence/fasta.py Wed Feb 24 11:57:35 2010 -0500 @@ -0,0 +1,108 @@ +#Dan Blankenberg + +class fastaSequence( object ): + def __init__( self ): + self.identifier = None + self.sequence = '' #holds raw sequence string: no whitespace + def __len__( self ): + return len( self.sequence ) + def __str__( self ): + return "%s\n%s\n" % ( self.identifier, self.sequence ) + +class fastaReader( object ): + def __init__( self, fh ): + self.file = fh + def close( self ): + return self.file.close() + def next( self ): + line = self.file.readline() + #remove header comment lines + while line and line.startswith( '#' ): + line = self.file.readline() + if not line: + raise StopIteration + assert line.startswith( '>' ), "FASTA headers must start with >" + rval = fastaSequence() + rval.identifier = line.strip() + offset = self.file.tell() + while True: + line = self.file.readline() + if not line or line.startswith( '>' ): + if line: + self.file.seek( offset ) #this causes sequence id lines to be read twice, once to determine previous sequence end and again when getting actual sequence; can we cache this to prevent it from being re-read? + return rval + #454 qual test data that was used has decimal scores that don't have trailing spaces + #so we'll need to parse and build these sequences not based upon de facto standards + #i.e. in a less than ideal fashion + line = line.rstrip() + if ' ' in rval.sequence or ' ' in line: + rval.sequence = "%s%s " % ( rval.sequence, line ) + else: + rval.sequence += line + offset = self.file.tell() + def __iter__( self ): + while True: + yield self.next() + +class fastaNamedReader( object ): + def __init__( self, fh ): + self.file = fh + self.reader = fastaReader( self.file ) + self.offset_dict = {} + self.eof = False + def close( self ): + return self.file.close() + def get( self, sequence_id ): + rval = None + if sequence_id in self.offset_dict: + initial_offset = self.file.tell() + seq_offset = self.offset_dict[ sequence_id ].pop( 0 ) + if not self.offset_dict[ sequence_id ]: + del self.offset_dict[ sequence_id ] + self.file.seek( seq_offset ) + rval = self.reader.next() + self.file.seek( initial_offset ) + else: + while True: + offset = self.file.tell() + try: + fasta_seq = self.reader.next() + except StopIteration: + self.eof = True + break #eof, id not found, will return None + if fasta_seq.identifier == sequence_id: + rval = fasta_seq + break + else: + if fasta_seq.identifier not in self.offset_dict: + self.offset_dict[ fasta_seq.identifier ] = [] + self.offset_dict[ fasta_seq.identifier ].append( offset ) + return rval + def has_data( self ): + #returns a string representation of remaining data, or empty string (False) if no data remaining + eof = self.eof + count = 0 + rval = '' + if self.offset_dict: + count = sum( map( len, self.offset_dict.values() ) ) + if not eof: + offset = self.file.tell() + try: + fasta_seq = self.reader.next() + except StopIteration: + eof = True + self.file.seek( offset ) + if count: + rval = "There were %i known sequences not utilized. " % count + if not eof: + rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." ) + return rval + +class fastaWriter( object ): + def __init__( self, fh ): + self.file = fh + def write( self, fastq_read ): + #this will include SOLiD adapter base if applicable + self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) + def close( self ): + return self.file.close() diff -r 66ba0f2d6d32 -r aece26463c9d lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Wed Feb 24 10:42:36 2010 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Wed Feb 24 11:57:35 2010 -0500 @@ -514,15 +514,6 @@ def close( self ): return self.file.close() -class fastaWriter( object ): - def __init__( self, fh ): - self.file = fh - def write( self, fastq_read ): - #this will include SOLiD adapter base if applicable - self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) - def close( self ): - return self.file.close() - class fastqJoiner( object ): def __init__( self, format, force_quality_encoding = None ): self.format = format @@ -592,104 +583,6 @@ read2.description += "/2" return read1, read2 -class fastaSequence( ): - def __init__( self ): - self.identifier = None - self.sequence = '' #holds raw sequence string: no whitespace - def __len__( self ): - return len( self.sequence ) - def __str__( self ): - return "%s\n%s\n" % ( self.identifier, self.sequence ) - -class fastaReader( object ): - def __init__( self, fh ): - self.file = fh - def close( self ): - return self.file.close() - def next( self ): - line = self.file.readline() - #remove header comment lines - while line and line.startswith( '#' ): - line = self.file.readline() - if not line: - raise StopIteration - assert line.startswith( '>' ), "FASTA headers must start with >" - rval = fastaSequence() - rval.identifier = line.strip() - offset = self.file.tell() - while True: - line = self.file.readline() - if not line or line.startswith( '>' ): - if line: - self.file.seek( offset ) - return rval - #454 qual test data that was used has decimal scores that don't have trailing spaces - #so we'll need to parse and build these sequences not based upon de facto standards - #i.e. in a less than ideal fashion - line = line.rstrip() - if ' ' in rval.sequence or ' ' in line: - rval.sequence = "%s%s " % ( rval.sequence, line ) - else: - rval.sequence += line - offset = self.file.tell() - def __iter__( self ): - while True: - yield self.next() - -class fastaNamedReader( object ): - def __init__( self, fh ): - self.file = fh - self.reader = fastaReader( self.file ) - self.offset_dict = {} - self.eof = False - def close( self ): - return self.file.close() - def get( self, sequence_id ): - rval = None - if sequence_id in self.offset_dict: - initial_offset = self.file.tell() - seq_offset = self.offset_dict[ sequence_id ].pop( 0 ) - if not self.offset_dict[ sequence_id ]: - del self.offset_dict[ sequence_id ] - self.file.seek( seq_offset ) - rval = self.reader.next() - self.file.seek( initial_offset ) - else: - while True: - offset = self.file.tell() - try: - fasta_seq = self.reader.next() - except StopIteration: - self.eof = True - break #eof, id not found, will return None - if fasta_seq.identifier == sequence_id: - rval = fasta_seq - break - else: - if fasta_seq.identifier not in self.offset_dict: - self.offset_dict[ fasta_seq.identifier ] = [] - self.offset_dict[ fasta_seq.identifier ].append( offset ) - return rval - def has_data( self ): - #returns a string representation of remaining data, or empty string (False) if no data remaining - eof = self.eof - count = 0 - rval = '' - if self.offset_dict: - count = sum( map( len, self.offset_dict.values() ) ) - if not eof: - offset = self.file.tell() - try: - fasta_seq = self.reader.next() - except StopIteration: - eof = True - self.file.seek( offset ) - if count: - rval = "There were %i known sequences not utilized. " % count - if not eof: - rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." ) - return rval - class fastqCombiner( object ): def __init__( self, format ): self.format = format diff -r 66ba0f2d6d32 -r aece26463c9d tools/fastq/fastq_combiner.py --- a/tools/fastq/fastq_combiner.py Wed Feb 24 10:42:36 2010 -0500 +++ b/tools/fastq/fastq_combiner.py Wed Feb 24 11:57:35 2010 -0500 @@ -1,6 +1,7 @@ #Dan Blankenberg import sys, os, shutil -from galaxy_utils.sequence.fastq import fastqWriter, fastaReader, fastaNamedReader, fastqSequencingRead, fastqCombiner +from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner +from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader def main(): #Read command line arguments diff -r 66ba0f2d6d32 -r aece26463c9d tools/fastq/fastq_to_fasta.py --- a/tools/fastq/fastq_to_fasta.py Wed Feb 24 10:42:36 2010 -0500 +++ b/tools/fastq/fastq_to_fasta.py Wed Feb 24 11:57:35 2010 -0500 @@ -1,6 +1,7 @@ #Dan Blankenberg import sys -from galaxy_utils.sequence.fastq import fastqReader, fastaWriter +from galaxy_utils.sequence.fastq import fastqReader +from galaxy_utils.sequence.fasta import fastaWriter def main(): input_filename = sys.argv[1]

1 0

Google Summer of Code proposal for phylogeny work with NESCent
by Brad Chapman 25 Feb '10

25 Feb '10

Galaxy folks; Would y'all be interested in writing up a Galaxy proposal for Google's Summer of Code? NESCent is planning to apply for the program this year; they've been a mentoring organization for the last 3 years, sponsoring students to work on phyloinformatics code, and I was involved last year as a mentor. Here is some background from last year's projects: https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code… They are starting now to get together the application for 2010, and one of the first steps in that process is generating proposals that students can apply for. I was thinking of including a proposal for integrating additional phylogenetic tools into Galaxy, and wanted to gauge your interest. Right now this is at the brainstorming level, but the general idea would be to build off of the tools already present for metagenome analysis. This could include anything from writing up XML files to include additional stand alone phylogenetic programs, coding up scripts or workflows to automate common analyses, and integrating visualization tools for trees like the InfoVis toolkit: http://thejit.org/ What do you think? If we get accepted and move forward it would be great to have someone from the Galaxy team to help with both formulating the project plans and mentoring during the summer. It's a great opportunity to have an excellent student working on Galaxy full time during the summer. Brad

3 3

[hg] galaxy 3435: lims:
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c1d024e76c2c changeset: 3435:c1d024e76c2c user: rc date: Wed Feb 24 10:04:03 2010 -0500 description: lims: - added error msg when dataset transfer is started for samples with no library - fixed typos - now dataset transfer does not affect sample state - request completion logic restored. diffstat: lib/galaxy/model/__init__.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 28 +++++++++++++++-------- scripts/galaxy_messaging/server/data_transfer.py | 2 +- templates/admin/requests/get_data.mako | 4 +- templates/admin/requests/show_request.mako | 8 +------ templates/base_panels.mako | 1 + templates/requests/show_request.mako | 2 +- 7 files changed, 25 insertions(+), 22 deletions(-) diffs (159 lines): diff -r 80747406525d -r c1d024e76c2c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Feb 24 08:44:22 2010 -0500 +++ b/lib/galaxy/model/__init__.py Wed Feb 24 10:04:03 2010 -0500 @@ -1414,7 +1414,7 @@ if self.events: return self.events[0].state return None - def untransfered_dataset_files(self): + def untransferred_dataset_files(self): count = 0 for df, status in self.dataset_files: if status == self.transfer_status.NOT_STARTED: diff -r 80747406525d -r c1d024e76c2c lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Feb 24 08:44:22 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Feb 24 10:04:03 2010 -0500 @@ -1275,8 +1275,8 @@ if s.current_state().id != request.type.states[-1].id: complete = False if request.complete() and not complete: - comments = "Sample(s) " % request.type.states[-1].name - event = trans.app.model.RequestEvent(request, request.states.COMPLETE, comments) + comments = "One or more samples moved back from the %s state" % request.type.states[-1].name + event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments) trans.sa_session.add( event ) trans.sa_session.flush() elif complete: @@ -1325,7 +1325,7 @@ event = trans.app.model.SampleEvent(sample, new_state, comments) trans.sa_session.add( event ) trans.sa_session.flush() - #self.__set_request_state( trans, sample.request ) + self.__set_request_state( trans, sample.request ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)) @@ -1370,6 +1370,14 @@ status='error', message="Invalid sample ID", **kwd) ) + # check if a library and folder has been set for this sample yet. + if not sample.library or not sample.folder: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + messagetype='error', + msg="Set a data library and folder for <b>%s</b> to transfer dataset(s)." % sample.name, + id=trans.security.encode_id(sample.request.id) ) ) if sample.request.type.datatx_info.get('data_dir', ''): folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') ) else: @@ -1405,7 +1413,7 @@ sample_id=trans.security.encode_id(sample.id), msg=msg, messagetype='error', folder_path=folder_path )) - return output.split()[2:] + return output.split() def __get_files_in_dir(self, trans, sample, folder_path): tmpfiles = self.__get_files(trans, sample, folder_path) @@ -1581,12 +1589,12 @@ dataset_index=index, cmd=cmd) dtt.start() - # set the sample state to the last state - if sample.current_state().id != sample.request.type.states[-1].id: - event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1], - 'The dataset is ready and are being transfered to Galaxy') - trans.sa_session.add( event ) - trans.sa_session.flush() +# # set the sample state to the last state +# if sample.current_state().id != sample.request.type.states[-1].id: +# event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1], +# 'The dataset is ready and are being transferred to Galaxy') +# trans.sa_session.add( event ) +# trans.sa_session.flush() if error_msg: return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_datatx_page', diff -r 80747406525d -r c1d024e76c2c scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Wed Feb 24 08:44:22 2010 -0500 +++ b/scripts/galaxy_messaging/server/data_transfer.py Wed Feb 24 10:04:03 2010 -0500 @@ -94,7 +94,7 @@ # update the data transfer status in the db self.update_status('Complete') # cleanup - self.cleanup() + #self.cleanup() sys.exit(0) def cleanup(self): diff -r 80747406525d -r c1d024e76c2c templates/admin/requests/get_data.mako --- a/templates/admin/requests/get_data.mako Wed Feb 24 08:44:22 2010 -0500 +++ b/templates/admin/requests/get_data.mako Wed Feb 24 10:04:03 2010 -0500 @@ -30,7 +30,7 @@ <h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3> <ul class="manage-table-actions"> -## %if sample.request.submitted() and sample.untransfered_dataset_files(): +## %if sample.request.submitted() and sample.untransferred_dataset_files(): ## <li> ## <a class="action-button" href="${h.url_for( controller='requests_admin', action='start_datatx', id=trans.security.encode_id(sample.id) )}"> ## <span>Start data transfer</span></a> @@ -60,7 +60,7 @@ <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" > %if len(dataset_files): <div class="form-row"> - <h4>Datasets Transfered</h4> + <h4>Datasets Transferred</h4> <div class="form-row"> <table class="grid"> <thead> diff -r 80747406525d -r c1d024e76c2c templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Wed Feb 24 08:44:22 2010 -0500 +++ b/templates/admin/requests/show_request.mako Wed Feb 24 10:04:03 2010 -0500 @@ -72,12 +72,6 @@ <span>Reject request</span></a> </li> %endif -## %if request.submitted() and request.samples: -## <li> -## <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> -## <span>Bar codes</span></a> -## </li> -## %endif <li> <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> <span>History</span></a> @@ -134,7 +128,7 @@ <th>Data Library</th> <th>Folder</th> %if request.submitted() or request.complete(): - <th>Dataset(s) Transfered</th> + <th>Dataset(s) Transferred</th> %endif <th></th> </tr> diff -r 80747406525d -r c1d024e76c2c templates/base_panels.mako --- a/templates/base_panels.mako Wed Feb 24 08:44:22 2010 -0500 +++ b/templates/base_panels.mako Wed Feb 24 10:04:03 2010 -0500 @@ -188,6 +188,7 @@ <div class="submenu"> <ul> <li><a href="${h.url_for( controller='/requests', action='index' )}">Sequencing Requests</a></li> + <li><a target="_blank" href="${app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rc/p/sts" )}">Help</a></li> </ul> </div> </td> diff -r 80747406525d -r c1d024e76c2c templates/requests/show_request.mako --- a/templates/requests/show_request.mako Wed Feb 24 08:44:22 2010 -0500 +++ b/templates/requests/show_request.mako Wed Feb 24 10:04:03 2010 -0500 @@ -124,7 +124,7 @@ <th>Data Library</th> <th>Folder</th> %if request.submitted() or request.complete(): - <th>Dataset(s) Transfered</th> + <th>Dataset(s) Transferred</th> %endif <th></th> </tr>

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[hg] galaxy 3436: lims:
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/66ba0f2d6d32 changeset: 3436:66ba0f2d6d32 user: rc date: Wed Feb 24 10:42:36 2010 -0500 description: lims: - code cleanup - cleanup tmp files after data transfer diffstat: lib/galaxy/web/controllers/requests_admin.py | 6 ------ scripts/galaxy_messaging/server/data_transfer.py | 2 +- 2 files changed, 1 insertions(+), 7 deletions(-) diffs (28 lines): diff -r c1d024e76c2c -r 66ba0f2d6d32 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Feb 24 10:04:03 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Feb 24 10:42:36 2010 -0500 @@ -1589,12 +1589,6 @@ dataset_index=index, cmd=cmd) dtt.start() -# # set the sample state to the last state -# if sample.current_state().id != sample.request.type.states[-1].id: -# event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1], -# 'The dataset is ready and are being transferred to Galaxy') -# trans.sa_session.add( event ) -# trans.sa_session.flush() if error_msg: return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_datatx_page', diff -r c1d024e76c2c -r 66ba0f2d6d32 scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Wed Feb 24 10:04:03 2010 -0500 +++ b/scripts/galaxy_messaging/server/data_transfer.py Wed Feb 24 10:42:36 2010 -0500 @@ -94,7 +94,7 @@ # update the data transfer status in the db self.update_status('Complete') # cleanup - #self.cleanup() + self.cleanup() sys.exit(0) def cleanup(self):

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[hg] galaxy 3434: Adding missing sam_merge test files
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/80747406525d changeset: 3434:80747406525d user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Feb 24 08:44:22 2010 -0500 description: Adding missing sam_merge test files diffstat: test-data/sam_merge_in1.bam | 0 test-data/sam_merge_in2.bam | 0 test-data/sam_merge_in3.bam | 0 test-data/sam_merge_out2.bam | 0 4 files changed, 0 insertions(+), 0 deletions(-) diffs (8 lines): diff -r 5fa69a40e080 -r 80747406525d test-data/sam_merge_in1.bam Binary file test-data/sam_merge_in1.bam has changed diff -r 5fa69a40e080 -r 80747406525d test-data/sam_merge_in2.bam Binary file test-data/sam_merge_in2.bam has changed diff -r 5fa69a40e080 -r 80747406525d test-data/sam_merge_in3.bam Binary file test-data/sam_merge_in3.bam has changed diff -r 5fa69a40e080 -r 80747406525d test-data/sam_merge_out2.bam Binary file test-data/sam_merge_out2.bam has changed

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adding local data
by Roy Weckiewicz 24 Feb '10

24 Feb '10

Hello, Thanks to the help of galaxy-dev, I've been able to migrate into a MySQL backend for my local galaxy instance. My next goal is to add the datasets for different genomes (bacterial, fungal, etc), so I've decided to start with human. I started out following the wiki Data Integration page and downloaded the BigZip files (full data set) for hg19. Next, the guide mentions to check individual tool xml's to see which .location file it uses, which in turn can be used to get the file type and format needed for the file. My first question: Is this the best way to go about adding a genome to a local instance -- Are the database files just referenced by the tools that use them, or is it possible to somehow include them in the MySQL database. Ideally I'd like to be able to select MyGenome from within Galaxy (probably through 'get Data' in the table browser ). The problem I'm having is that I cannot find all of the required files for a lot of the tools that came with the galaxy installation. Are a lot of these files just the resulting output of a script or program? e.g. ENCODE data, sequence alignments, genomic DNA extraction, etc. Best Regards, Roy Weckiewicz -- Roy Weckiewicz Texas A&M University

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[hg] galaxy 3433: Updated Bowtie test files to handle new versio...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5fa69a40e080 changeset: 3433:5fa69a40e080 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Feb 24 07:11:43 2010 -0500 description: Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools. diffstat: test-data/bowtie_in1.fastqsanger | 4 ++-- test-data/bowtie_out1.sam | 2 +- test-data/bowtie_out3.sam | 4 ++-- test-data/bowtie_out5.sam | 2 +- test-data/bowtie_out7.sam | 4 ++-- test-data/sam_to_bam_out1.bam | 0 tools/samtools/sam_merge.xml | 2 +- tools/samtools/sam_pileup.xml | 2 +- tools/samtools/sam_to_bam.xml | 2 +- tools/sr_mapping/bowtie_color_wrapper.xml | 30 ++++++++++++++---------------- tools/sr_mapping/bowtie_wrapper.xml | 30 ++++++++++++++---------------- tools/sr_mapping/bwa_wrapper.xml | 2 -- 12 files changed, 39 insertions(+), 45 deletions(-) diffs (223 lines): diff -r b4dd38c06398 -r 5fa69a40e080 test-data/bowtie_in1.fastqsanger --- a/test-data/bowtie_in1.fastqsanger Tue Feb 23 23:17:09 2010 -0500 +++ b/test-data/bowtie_in1.fastqsanger Wed Feb 24 07:11:43 2010 -0500 @@ -1,4 +1,4 @@ @869_1532_1255/1 -G21022233110003122233210021301222000112122113330022 +G2102223311000312223321002 + -=;8:?@=?;;9:8;=>;5A?;<8><<=:9><;9<=8;96>8<5==:<98; \ No newline at end of file +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r b4dd38c06398 -r 5fa69a40e080 test-data/bowtie_out1.sam --- a/test-data/bowtie_out1.sam Tue Feb 23 23:17:09 2010 -0500 +++ b/test-data/bowtie_out1.sam Wed Feb 24 07:11:43 2010 -0500 @@ -1,1 +1,1 @@ -869_1532_1255/1 16 chrM 3728 255 48M * 0 0 GAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAGAGG "TUVYQPSUSNSRTXTSVYVRVXWYUSVY_UOXZWRQRSUY[\^XQR! XA:i:1 MD:Z:48 NM:i:0 CM:i:2 +869_1532_1255/1 16 chrM 3753 255 23M * 0 0 TTTGATAGAGTAAAACATAGAGG YUSVY_UOXZWRQRSUY[\^XQ! XA:i:1 MD:Z:23 NM:i:0 CM:i:1 diff -r b4dd38c06398 -r 5fa69a40e080 test-data/bowtie_out3.sam --- a/test-data/bowtie_out3.sam Tue Feb 23 23:17:09 2010 -0500 +++ b/test-data/bowtie_out3.sam Wed Feb 24 07:11:43 2010 -0500 @@ -1,2 +1,2 @@ -869_1532_1255 179 chrM 3727 255 25M = 3752 50 GGAAATATGTCTGACAAAAGAGTTA !!RVYVSTXTRSNSUSPQYVUTPR; XA:i:1 MD:Z:25 NM:i:0 CM:i:1 -869_1532_1255 115 chrM 3752 255 25M = 3727 -50 CTTTGATAGAGTAAAACATAGAGGC >USVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1 +869_1532_1255 179 chrM 3727 255 25M = 3752 50 GGAAATATGTCTGACAAAAGAGTTA !"VRVYVSTXTRSNSUSPQYVUTP8 XA:i:1 MD:Z:25 NM:i:0 CM:i:1 +869_1532_1255 115 chrM 3752 255 25M = 3727 -50 CTTTGATAGAGTAAAACATAGAGGC <YUSVY_UOXZWRQRSUY[\^XQ!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1 diff -r b4dd38c06398 -r 5fa69a40e080 test-data/bowtie_out5.sam --- a/test-data/bowtie_out5.sam Tue Feb 23 23:17:09 2010 -0500 +++ b/test-data/bowtie_out5.sam Wed Feb 24 07:11:43 2010 -0500 @@ -1,1 +1,1 @@ -869_1532_1255/1 16 chrM 3727 255 50M * 0 0 GGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAGAGGC !"TUVYQPSUSNSRTXTSVYVRVXWYUSVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:50 NM:i:0 CM:i:2 +869_1532_1255/1 16 chrM 3752 255 25M * 0 0 CTTTGATAGAGTAAAACATAGAGGC <YUSVY_UOXZWRQRSUY[\^XQ!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1 diff -r b4dd38c06398 -r 5fa69a40e080 test-data/bowtie_out7.sam --- a/test-data/bowtie_out7.sam Tue Feb 23 23:17:09 2010 -0500 +++ b/test-data/bowtie_out7.sam Wed Feb 24 07:11:43 2010 -0500 @@ -1,2 +1,2 @@ -869_1532_1255 179 chrM 3728 255 23M = 3752 47 GAAATATGTCTGACAAAAGAGTT !RVYVSTXTRSNSUSPQYVUTPR XA:i:1 MD:Z:23 NM:i:0 CM:i:1 -869_1532_1255 115 chrM 3753 255 23M = 3727 -49 TTTGATAGAGTAAAACATAGAGG USVY_UOXZWRQRSUY[\^XQR! XA:i:1 MD:Z:23 NM:i:0 CM:i:1 +869_1532_1255 179 chrM 3728 255 23M = 3752 47 GAAATATGTCTGACAAAAGAGTT "VRVYVSTXTRSNSUSPQYVUTP XA:i:1 MD:Z:23 NM:i:0 CM:i:1 +869_1532_1255 115 chrM 3753 255 23M = 3727 -49 TTTGATAGAGTAAAACATAGAGG YUSVY_UOXZWRQRSUY[\^XQ! XA:i:1 MD:Z:23 NM:i:0 CM:i:1 diff -r b4dd38c06398 -r 5fa69a40e080 test-data/sam_to_bam_out1.bam Binary file test-data/sam_to_bam_out1.bam has changed diff -r b4dd38c06398 -r 5fa69a40e080 tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/samtools/sam_merge.xml Wed Feb 24 07:11:43 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="sam_merge" name="Merge BAM Files" version="1.0.0"> +<tool id="sam_merge" name="Merge BAM Files" version="1.1.0"> <description>merges BAM files together</description> <command interpreter="python"> sam_merge.py diff -r b4dd38c06398 -r 5fa69a40e080 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/samtools/sam_pileup.xml Wed Feb 24 07:11:43 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="sam_pileup" name="Generate pileup" version="1.0.0"> +<tool id="sam_pileup" name="Generate pileup" version="1.1.0"> <description>from BAM dataset</description> <command interpreter="python"> sam_pileup.py diff -r b4dd38c06398 -r 5fa69a40e080 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/samtools/sam_to_bam.xml Wed Feb 24 07:11:43 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="1.0.0"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0"> <description>converts SAM format to BAM format</description> <command interpreter="python"> sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} diff -r b4dd38c06398 -r 5fa69a40e080 tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Feb 24 07:11:43 2010 -0500 @@ -197,12 +197,12 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="bowtie_indices_color.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> + <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_file="bowtie_indices_color.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> @@ -252,7 +252,7 @@ </when>  </conditional>  </when>  - </conditional>  + </conditional>  <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> @@ -262,9 +262,9 @@ <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="sParams"> <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> @@ -327,9 +327,9 @@ </param> <conditional name="pParams"> <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> @@ -417,7 +417,7 @@  @@ -533,8 +533,6 @@ Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. -This tool uses Bowtie version 0.12.1. - .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml ------ diff -r b4dd38c06398 -r 5fa69a40e080 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Wed Feb 24 07:11:43 2010 -0500 @@ -191,13 +191,13 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - </when> + <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> + </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> <conditional name="indexParams"> @@ -246,7 +246,7 @@ </when>  </conditional>  </when>  - </conditional>  + </conditional>  <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> @@ -256,9 +256,9 @@ <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="sParams"> <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> @@ -315,9 +315,9 @@ </param> <conditional name="pParams"> <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> @@ -506,8 +506,6 @@ Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. -This tool uses Bowtie version 0.12.1. - .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml ------ diff -r b4dd38c06398 -r 5fa69a40e080 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Tue Feb 23 23:17:09 2010 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Wed Feb 24 07:11:43 2010 -0500 @@ -181,8 +181,6 @@ BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. -This tool uses BWA version 0.5.5. - ------ **Know what you are doing**

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