3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/22ef970cfdcd/ changeset: 22ef970cfdcd user: jgoecks date: 2012-12-18 18:02:56 summary: Use slideUp rather than hide for pretty hiding of HDAs when re= moved. affected #: 2 files diff -r 166303bbdd86eefc263d9947b35c65ec3847ddc9 -r 22ef970cfdcd9c82841634e= d2dcfff4a4ae14c04 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -119,7 +119,7 @@ icon_class : 'delete', on_click : function() { // Provide feedback by hiding from view immediately. - self.$el.hide(); + self.$el.slideUp(); =20 // Delete the dataset on the server and update HDA + view = depending on success/failure. // FIXME: when HDA-delete is implemented in the API, can c= all set(), then save directly=20 diff -r 166303bbdd86eefc263d9947b35c65ec3847ddc9 -r 22ef970cfdcd9c82841634e= d2dcfff4a4ae14c04 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=3DHDABaseView.extend(LoggableMixin).extend({initialize:fun= ction(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryA= ctionButtonRenderers=3D[this._render_showParamsButton,this._render_rerunBut= ton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.template= s.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_title= Buttons:function(){var a=3D$('<div class=3D"historyItemButtons"></div>');a.= append(this._render_displayButton());a.append(this._render_editButton());a.= append(this._render_deleteButton());return a},_render_editButton:function()= {if((this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STATES.UPLOA= D)||(this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STATES.NOT_V= IEWABLE)||(!this.model.get("accessible"))){this.editButton=3Dnull;return nu= ll}var c=3Dthis.model.get("purged"),a=3Dthis.model.get("deleted"),b=3D{titl= e:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class= :"edit"};if(a||c){b.enabled=3Dfalse;if(c){b.title=3D_l("Cannot edit attribu= tes of datasets removed from disk")}else{if(a){b.title=3D_l("Undelete datas= et to edit attributes")}}}this.editButton=3Dnew IconButtonView({model:new I= conButton(b)});return this.editButton.render().$el},_render_deleteButton:fu= nction(){if((this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STAT= ES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=3Dnull= ;return null}var a=3Dthis,b=3Da.urls["delete"],c=3D{title:_l("Delete"),href= :b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_cli= ck:function(){a.$el.hide();$.ajax({url:b,type:"POST",error:function(){a.$el= .show()},success:function(){a.model.set("deleted",true);a.$el.remove()}});r= eturn false}};if(this.model.get("deleted")||this.model.get("purged")){c=3D{= title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}t= his.deleteButton=3Dnew IconButtonView({model:new IconButton(c)});return thi= s.deleteButton.render().$el},_render_hdaSummary:function(){var a=3D_.extend= (this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")= =3D=3D=3D"?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_an= d_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errBu= tton:function(){if(this.model.get("state")!=3D=3DHistoryDatasetAssociation.= STATES.ERROR){this.errButton=3Dnull;return null}this.errButton=3Dnew IconBu= ttonView({model:new IconButton({title:_l("View or report this error"),href:= this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return thi= s.errButton.render().$el},_render_rerunButton:function(){this.rerunButton= =3Dnew IconButtonView({model:new IconButton({title:_l("Run this job again")= ,href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});re= turn this.rerunButton.render().$el},_render_visualizationsButton:function()= {var c=3Dthis.model.get("dbkey"),a=3Dthis.model.get("visualizations"),f=3Dt= his.urls.visualization,d=3D{},g=3D{dataset_id:this.model.get("id"),hda_ldda= :"hda"};if(c){g.dbkey=3Dc}if(!(this.model.hasData())||!(a&&a.length)||!(f))= {this.visualizationsButton=3Dnull;return null}this.visualizationsButton=3Dn= ew IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_= class:"chart_curve"})});var b=3Dthis.visualizationsButton.render().$el;b.ad= dClass("visualize-icon");function e(h){switch(h){case"trackster":return cre= ate_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_= action_fn(f,g);default:return function(){window.parent.location=3Df+"/"+h+"= ?"+$.param(g)}}}if(a.length=3D=3D=3D1){b.attr("title",a[0]);b.click(e(a[0])= )}else{_.each(a,function(i){var h=3Di.charAt(0).toUpperCase()+i.slice(1);d[= _l(h)]=3De(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButton= s:function(b){var c=3D$("<div/>"),a=3Dthis;c.attr("style","float: right;").= attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c= .append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model= .hasData())||(!this.urls.tags.get)){this.tagButton=3Dnull;return null}this.= tagButton=3Dnew IconButtonView({model:new IconButton({title:_l("Edit datase= t tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})})= ;return this.tagButton.render().$el},_render_annotateButton:function(){if(!= (this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=3D= null;return null}this.annotateButton=3Dnew IconButtonView({model:new IconBu= tton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"= annotate"})});return this.annotateButton.render().$el},_render_tagArea:func= tion(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.t= agArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotation= Area:function(){if(!this.urls.annotation.get){return null}return $(HDAEditV= iew.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})= ))},_render_body_error:function(a){HDABaseView.prototype._render_body_error= .call(this,a);var b=3Da.find("#primary-actions-"+this.model.get("id"));b.pr= epend(this._render_errButton())},_render_body_ok:function(a){a.append(this.= _render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._ren= der_primaryActionButtons([this._render_downloadButton,this._render_showPara= msButton,this._render_rerunButton]));return}a.append(this._render_primaryAc= tionButtons([this._render_downloadButton,this._render_showParamsButton,this= ._render_rerunButton,this._render_visualizationsButton]));a.append(this._re= nder_secondaryActionButtons([this._render_tagButton,this._render_annotateBu= tton]));a.append('<div class=3D"clear"/>');a.append(this._render_tagArea())= ;a.append(this._render_annotationArea());a.append(this._render_displayApps(= ));a.append(this._render_peek())},events:{"click .historyItemTitle":"toggle= BodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.ic= on-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function= (b){this.log(this+".loadAndDisplayTags",b);var c=3Dthis.$el.find(".tag-area= "),a=3Dc.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.= ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},= success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fas= t")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadA= ndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b= );var d=3Dthis.$el.find(".annotation-area"),c=3Dd.find(".annotation-elt"),a= =3Dthis.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){= $.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations= failed"))},success:function(e){if(e=3D=3D=3D""){e=3D"<em>"+_l("Describe or= add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();asyn= c_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slide= Down("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return fal= se},toString:function(){var a=3D(this.model)?(this.model+""):("(no model)")= ;return"HDAView("+a+")"}});HDAEditView.templates=3D{tagArea:Handlebars.temp= lates["template-hda-tagArea"],annotationArea:Handlebars.templates["template= -hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=3D= function(){var d=3D$(window.parent.document).find("iframe#galaxy_main"),c= =3Da+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").re= move();return false};return action}function create_trackster_action_fn(a,c,= b){return function(){var d=3D{};if(b){d["f-dbkey"]=3Db}$.ajax({url:a+"/list= _tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not a= dd this dataset to browser")+".")},success:function(e){var f=3Dwindow.paren= t;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:f= unction(){f.hide_modal()},"View in saved visualization":function(){f.show_m= odal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_moda= l()},"Add to visualization":function(){$(f.document).find("input[name=3Did]= :checked").each(function(){var g=3D$(this).val();c.id=3Dg;f.location=3Da+"/= trackster?"+$.param(c)})}})},"View in new visualization":function(){f.locat= ion=3Da+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=3DHDABaseView.extend(LoggableMixin).extend({initialize:fun= ction(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryA= ctionButtonRenderers=3D[this._render_showParamsButton,this._render_rerunBut= ton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.template= s.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_title= Buttons:function(){var a=3D$('<div class=3D"historyItemButtons"></div>');a.= append(this._render_displayButton());a.append(this._render_editButton());a.= append(this._render_deleteButton());return a},_render_editButton:function()= {if((this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STATES.UPLOA= D)||(this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STATES.NOT_V= IEWABLE)||(!this.model.get("accessible"))){this.editButton=3Dnull;return nu= ll}var c=3Dthis.model.get("purged"),a=3Dthis.model.get("deleted"),b=3D{titl= e:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class= :"edit"};if(a||c){b.enabled=3Dfalse;if(c){b.title=3D_l("Cannot edit attribu= tes of datasets removed from disk")}else{if(a){b.title=3D_l("Undelete datas= et to edit attributes")}}}this.editButton=3Dnew IconButtonView({model:new I= conButton(b)});return this.editButton.render().$el},_render_deleteButton:fu= nction(){if((this.model.get("state")=3D=3D=3DHistoryDatasetAssociation.STAT= ES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=3Dnull= ;return null}var a=3Dthis,b=3Da.urls["delete"],c=3D{title:_l("Delete"),href= :b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_cli= ck:function(){a.$el.slideUp();$.ajax({url:b,type:"POST",error:function(){a.= $el.show()},success:function(){a.model.set("deleted",true);a.$el.remove()}}= );return false}};if(this.model.get("deleted")||this.model.get("purged")){c= =3D{title:_l("Dataset is already deleted"),icon_class:"delete",enabled:fals= e}}this.deleteButton=3Dnew IconButtonView({model:new IconButton(c)});return= this.deleteButton.render().$el},_render_hdaSummary:function(){var a=3D_.ex= tend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbke= y")=3D=3D=3D"?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown= _and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_er= rButton:function(){if(this.model.get("state")!=3D=3DHistoryDatasetAssociati= on.STATES.ERROR){this.errButton=3Dnull;return null}this.errButton=3Dnew Ico= nButtonView({model:new IconButton({title:_l("View or report this error"),hr= ef:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return = this.errButton.render().$el},_render_rerunButton:function(){this.rerunButto= n=3Dnew IconButtonView({model:new IconButton({title:_l("Run this job again"= ),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});r= eturn this.rerunButton.render().$el},_render_visualizationsButton:function(= ){var c=3Dthis.model.get("dbkey"),a=3Dthis.model.get("visualizations"),f=3D= this.urls.visualization,d=3D{},g=3D{dataset_id:this.model.get("id"),hda_ldd= a:"hda"};if(c){g.dbkey=3Dc}if(!(this.model.hasData())||!(a&&a.length)||!(f)= ){this.visualizationsButton=3Dnull;return null}this.visualizationsButton=3D= new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon= _class:"chart_curve"})});var b=3Dthis.visualizationsButton.render().$el;b.a= ddClass("visualize-icon");function e(h){switch(h){case"trackster":return cr= eate_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot= _action_fn(f,g);default:return function(){window.parent.location=3Df+"/"+h+= "?"+$.param(g)}}}if(a.length=3D=3D=3D1){b.attr("title",a[0]);b.click(e(a[0]= ))}else{_.each(a,function(i){var h=3Di.charAt(0).toUpperCase()+i.slice(1);d= [_l(h)]=3De(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButto= ns:function(b){var c=3D$("<div/>"),a=3Dthis;c.attr("style","float: right;")= .attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){= c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.mode= l.hasData())||(!this.urls.tags.get)){this.tagButton=3Dnull;return null}this= .tagButton=3Dnew IconButtonView({model:new IconButton({title:_l("Edit datas= et tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})}= );return this.tagButton.render().$el},_render_annotateButton:function(){if(= !(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton= =3Dnull;return null}this.annotateButton=3Dnew IconButtonView({model:new Ico= nButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_clas= s:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:f= unction(){if(!this.urls.tags.set){return null}return $(HDAEditView.template= s.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotat= ionArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEd= itView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.url= s})))},_render_body_error:function(a){HDABaseView.prototype._render_body_er= ror.call(this,a);var b=3Da.find("#primary-actions-"+this.model.get("id"));b= .prepend(this._render_errButton())},_render_body_ok:function(a){a.append(th= is._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._= render_primaryActionButtons([this._render_downloadButton,this._render_showP= aramsButton,this._render_rerunButton]));return}a.append(this._render_primar= yActionButtons([this._render_downloadButton,this._render_showParamsButton,t= his._render_rerunButton,this._render_visualizationsButton]));a.append(this.= _render_secondaryActionButtons([this._render_tagButton,this._render_annotat= eButton]));a.append('<div class=3D"clear"/>');a.append(this._render_tagArea= ());a.append(this._render_annotationArea());a.append(this._render_displayAp= ps());a.append(this._render_peek())},events:{"click .historyItemTitle":"tog= gleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a= .icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:funct= ion(b){this.log(this+".loadAndDisplayTags",b);var c=3Dthis.$el.find(".tag-a= rea"),a=3Dc.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html()))= {$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed")= )},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("= fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},lo= adAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation= ",b);var d=3Dthis.$el.find(".annotation-area"),c=3Dd.find(".annotation-elt"= ),a=3Dthis.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html()= )){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotati= ons failed"))},success:function(e){if(e=3D=3D=3D""){e=3D"<em>"+_l("Describe= or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();a= sync_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.sl= ideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return = false},toString:function(){var a=3D(this.model)?(this.model+""):("(no model= )");return"HDAView("+a+")"}});HDAEditView.templates=3D{tagArea:Handlebars.t= emplates["template-hda-tagArea"],annotationArea:Handlebars.templates["templ= ate-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action= =3Dfunction(){var d=3D$(window.parent.document).find("iframe#galaxy_main"),= c=3Da+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").r= emove();return false};return action}function create_trackster_action_fn(a,c= ,b){return function(){var d=3D{};if(b){d["f-dbkey"]=3Db}$.ajax({url:a+"/lis= t_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not = add this dataset to browser")+".")},success:function(e){var f=3Dwindow.pare= nt;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:= function(){f.hide_modal()},"View in saved visualization":function(){f.show_= modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_mod= al()},"Add to visualization":function(){$(f.document).find("input[name=3Did= ]:checked").each(function(){var g=3D$(this).val();c.id=3Dg;f.location=3Da+"= /trackster?"+$.param(c)})}})},"View in new visualization":function(){f.loca= tion=3Da+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/2462f311b8b8/ changeset: 2462f311b8b8 user: jgoecks date: 2012-12-18 18:08:47 summary: Add simple read group options for Bowtie2. affected #: 2 files diff -r 22ef970cfdcd9c82841634ed2dcfff4a4ae14c04 -r 2462f311b8b872ab875132f= fcc1a4347af8a5472 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -25,6 +25,12 @@ parser.add_option( '', '--local', dest=3D'local', action=3D"store_true= " ) parser.add_option( '', '--preset-alignment', dest=3D'preset_alignment') =20 + # Read group options. + parser.add_option( '', '--rgid', dest=3D'rgid', help=3D'Read group ide= ntifier' ) + parser.add_option( '', '--rglb', dest=3D'rglb', help=3D'Library name' ) + parser.add_option( '', '--rgpl', dest=3D'rgpl', help=3D'Platform/techn= ology used to produce the reads' ) + parser.add_option( '', '--rgsm', dest=3D'rgsm', help=3D'Sample' ) + (options, args) =3D parser.parse_args() =20 # Creat bowtie index if necessary. @@ -86,7 +92,16 @@ if options.local: opts +=3D ' --local' if options.preset_alignment: - opts +=3D " --" + options.preset_alignment + opts +=3D ' --' + options.preset_alignment + + # Read group options. + if options.rgid: + if not options.rglb or not options.rgpl or not options.rgsm: + stop_err( 'If you want to specify read groups, you must includ= e the ID, LB, PL, and SM tags.' ) + opts +=3D ' --rg-id %s' % options.rgid + opts +=3D ' --rg %s:%s' % ( 'LB', options.rglb ) + opts +=3D ' --rg %s:%s' % ( 'PL', options.rgpl ) + opts +=3D ' --rg %s:%s' % ( 'SM', options.rgsm ) =20 # Final command: cmd =3D cmd % ( opts, index_path, reads, options.output ) diff -r 22ef970cfdcd9c82841634ed2dcfff4a4ae14c04 -r 2462f311b8b872ab875132f= fcc1a4347af8a5472 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -44,6 +44,14 @@ --local --preset-alignment=3D$params.preset.align_preset_s= elect-local #end if #end if + + ## Read group information. + #if $params.readGroup.specReadGroup =3D=3D "yes" + --rgid=3D"$params.readGroup.rgid" + --rglb=3D"$params.readGroup.rglb" + --rgpl=3D"$params.readGroup.rgpl" + --rgsm=3D"$params.readGroup.rgsm" + #end if </command><inputs><conditional name=3D"singlePaired"> @@ -80,7 +88,7 @@ </when><!-- history --></conditional><!-- refGenomeSource --><co= nditional name=3D"params"> - <param name=3D"settingsType" type=3D"select" label=3D"Bowtie s= ettings to use" help=3D"You can use the default settings or set custom valu= es for any of Bowtie's parameters."> + <param name=3D"settingsType" type=3D"select" label=3D"Paramete= r Settings" help=3D"You can use the default settings or set custom values f= or any of Bowtie's parameters."><option value=3D"preSet">Use Defaults</opti= on><option value=3D"full">Full parameter list</option></param> @@ -104,9 +112,21 @@ <option value=3D"very-sensitive">Very sensitiv= e</option></param></when> - <!-- TODO: --><when value=3D"No" /></conditional> + <conditional name=3D"readGroup"> + <param name=3D"specReadGroup" type=3D"select" label=3D"Spe= cify the read group for this file?"> + <option value=3D"yes">Yes</option> + <option value=3D"no" selected=3D"True">No</option> + </param> + <when value=3D"yes"> + <param name=3D"rgid" type=3D"text" size=3D"25" label= =3D"Read group identi=EF=AC=81er (ID). Each @RG line must have a unique ID.= The value of ID is used in the RG tags of alignment records. Must be uniqu= e among all read groups in header section." help=3D"Required if RG specifie= d. Read group IDs may be modi=EF=AC=81ed when merging SAM =EF=AC=81les in o= rder to handle collisions." /> + <param name=3D"rglb" type=3D"text" size=3D"25" label= =3D"Library name (LB)" help=3D"Required if RG specified" /> + <param name=3D"rgpl" type=3D"text" size=3D"25" label= =3D"Platform/technology used to produce the reads (PL)" help=3D"Required if= RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, I= ONTORRENT and PACBIO" /> + <param name=3D"rgsm" type=3D"text" size=3D"25" label= =3D"Sample (SM)" help=3D"Required if RG specified. Use pool name where a po= ol is being sequenced" /> + </when> + <when value=3D"no" /> + </conditional></when><!-- full --></conditional><!-- params --=

</inputs>

https://bitbucket.org/galaxy/galaxy-central/changeset/8e1eec8c56cc/ changeset: 8e1eec8c56cc user: jgoecks date: 2012-12-18 18:09:11 summary: Automated merge. affected #: 1 file diff -r 2462f311b8b872ab875132ffcc1a4347af8a5472 -r 8e1eec8c56cc5f62f5541c7= 54f31607675347285 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1488,7 +1488,7 @@ if shed_tool_conf =3D=3D shed_tool_conf_dict[ 'config_filename' ]: return index, shed_tool_conf_dict else: - file_name =3D suc.strip_path( shed_tool_conf_dict[ 'config_fil= ename' ] ) + file_name =3D strip_path( shed_tool_conf_dict[ 'config_filenam= e' ] ) if shed_tool_conf =3D=3D file_name: return index, shed_tool_conf_dict def get_tool_panel_config_tool_path_install_dir( app, repository ): 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.