[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ba68bb089e1/ Changeset: 3ba68bb089e1 User: dannon Date: 2014-08-06 16:16:22 Summary: Fix for conditionally using bucket_default in cloudlaunch. Affected #: 1 file diff -r 33c032a19f9af4549a5dfa7a55df7883117b4ea8 -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -70,10 +70,18 @@ cfg = cloudman.CloudManConfig(key_id, secret, cluster_name, ami, instance_type, password, placement=zone) cml = cloudman.launch.CloudManLauncher(key_id, secret) - result = cml.launch(cluster_name, ami, instance_type, password, - cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, - cfg.security_groups, cfg.placement, - bucket_default=bucket_default) + # This should probably be handled better on the bioblend side, but until + # an egg update can be made, this needs to conditionally include the + # parameter or not, even if the value is None. + if bucket_default: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement, + bucket_default=bucket_default) + else: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement) # result is a dict with sg_names, kp_name, kp_material, rs, and instance_id if not result['rs']: trans.response.status = 400 https://bitbucket.org/galaxy/galaxy-central/commits/08d1eb86cd6f/ Changeset: 08d1eb86cd6f User: dannon Date: 2014-08-06 16:16:55 Summary: Merge. Affected #: 30 files diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -37,7 +37,8 @@ var BaseCitationCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( { /** root api url */ urlRoot : galaxy_config.root + 'api', - model : Citation + partial : true, // Assume some tools in history/workflow may not be properly annotated yet. + model : Citation, } ); var HistoryCitationCollection = BaseCitationCollection.extend( { @@ -51,7 +52,8 @@ /** complete api url */ url : function() { return this.urlRoot + '/tools/' + this.tool_id + '/citations'; - } + }, + partial : false, // If a tool has citations, assume they are complete. } ); //============================================================================== diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -120,7 +120,7 @@ }, render: function() { - this.$el.html(this.citationsElement); + this.$el.html(this.citationsElement()); this.collection.each(function( item ){ this.renderCitation( item ); }, this); @@ -142,29 +142,40 @@ this.$(".citations-formatted").show(); }, - citationsElement: [ - '<div class="toolForm">', - '<div class="toolFormTitle">', - _l("Citations"), - ' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>', - ' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>', - '</div>', - '<div class="toolFormBody" style="padding:5px 10px">', - '<div style="padding:5px 10px">', - '<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate', - ' citations explicitly at this time. When writing up your analysis, please manually', - ' review your histories and find all references', - ' that should be cited in order to completely describe your work. Also, please remember to', - ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.', - '</div>', - '<span class="citations-formatted"></span>', - '</div>', - '<div class="citations-bibtex toolFormBody" style="padding:5px 10px">', - '<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>', - '</div>', - '</div>' - ].join( '' ) + partialWarningElement: function() { + if( this.collection.partial ) { + return [ + '<div style="padding:5px 10px">', + '<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate', + ' citations explicitly at this time. When writing up your analysis, please manually', + ' review your histories and find all references', + ' that should be cited in order to completely describe your work. Also, please remember to', + ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.', + '</div>', + ].join(''); + } else { + return ''; + } + }, + citationsElement: function() { + return [ + '<div class="toolForm">', + '<div class="toolFormTitle">', + _l("Citations"), + ' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>', + ' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>', + '</div>', + '<div class="toolFormBody" style="padding:5px 10px">', + this.partialWarningElement(), + '<span class="citations-formatted"></span>', + '</div>', + '<div class="citations-bibtex toolFormBody" style="padding:5px 10px">', + '<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>', + '</div>', + '</div>' + ].join( '' ); + } }); //============================================================================== diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a static/scripts/packed/mvc/citation/citation-model.js --- a/static/scripts/packed/mvc/citation/citation-model.js +++ b/static/scripts/packed/mvc/citation/citation-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",model:f});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"}});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return f?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement);this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},citationsElement:['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">','<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return f?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml +++ b/tools/maf/genebed_maf_to_fasta.xml @@ -1,5 +1,8 @@ <tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1"><description>given a set of coding exon intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} @@ -87,12 +90,7 @@ * stitches blocks together and resolves overlaps based on alignment score; * outputs alignments in FASTA format. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -1,5 +1,8 @@ <tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species @@ -283,12 +286,7 @@ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/interval2maf_pairwise.xml --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -1,5 +1,8 @@ <tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command><inputs><param name="input1" type="data" format="interval" label="Interval File"> @@ -39,12 +42,7 @@ .. image:: ${static_path}/images/maf_icons/interval2maf.png ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -1,5 +1,8 @@ <tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} @@ -103,12 +106,7 @@ .. image:: ${static_path}/images/maf_icons/stitchMaf.png ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/macros.xml --- /dev/null +++ b/tools/maf/macros.xml @@ -0,0 +1,16 @@ +<macros> + <token name="@HELP_CITATIONS@"> +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr398</citation> + </citations> + </xml> +</macros> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_by_block_number.xml --- a/tools/maf/maf_by_block_number.xml +++ b/tools/maf/maf_by_block_number.xml @@ -1,5 +1,8 @@ <tool id="maf_by_block_number1" name="Extract MAF by block number" version="1.0.1"><description>given a set of block numbers and a MAF file</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_by_block_number.py $input1 $input2 $out_file1 $block_col $species</command><inputs><param format="txt" name="input1" type="data" label="Block Numbers"/> @@ -29,12 +32,7 @@ This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_filter.xml --- a/tools/maf/maf_filter.xml +++ b/tools/maf/maf_filter.xml @@ -1,5 +1,8 @@ <tool id="MAF_filter" name="Filter MAF" version="1.0.1"><description>by specified attributes</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_filter.py $maf_filter_file $input1 $out_file1 $out_file1.files_path $species $min_size $max_size $min_species_per_block $exclude_incomplete_blocks ${input1.metadata.species}</command><inputs><page> @@ -191,12 +194,7 @@ You can also provide a size range and limit your output to the MAF blocks which fall within the specified range. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - -</help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_limit_size.xml --- a/tools/maf/maf_limit_size.xml +++ b/tools/maf/maf_limit_size.xml @@ -1,5 +1,8 @@ <tool id="maf_limit_size1" name="Filter MAF blocks" version="1.0.1"><description>by Size</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_limit_size.py $input1 $out_file1 $min_size $max_size</command><inputs><page> @@ -25,12 +28,7 @@ This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_limit_to_species.xml --- a/tools/maf/maf_limit_to_species.xml +++ b/tools/maf/maf_limit_to_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_Limit_To_Species1" name="Filter MAF blocks"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_limit_to_species.py $species $input1 $out_file1 $allow_partial $min_species</command><inputs><param name="input1" type="data" format="maf" label="MAF file"/> @@ -39,13 +42,8 @@ * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_reverse_complement.xml --- a/tools/maf/maf_reverse_complement.xml +++ b/tools/maf/maf_reverse_complement.xml @@ -1,5 +1,8 @@ <tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1"><description>a MAF file</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command><inputs><page> @@ -42,12 +45,7 @@ s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_split_by_species.xml --- a/tools/maf/maf_split_by_species.xml +++ b/tools/maf/maf_split_by_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_split_blocks_by_species1" name="Split MAF blocks" version="1.0.0"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_split_by_species.py $input1 $out_file1 $collapse_columns</command><inputs><param format="maf" name="input1" type="data" label="MAF file to split"/> @@ -211,13 +214,8 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_stats.xml --- a/tools/maf/maf_stats.xml +++ b/tools/maf/maf_stats.xml @@ -1,5 +1,8 @@ <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"><description>Alignment coverage information</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> maf_stats.py #if $maf_source_type.maf_source == "user": @@ -109,12 +112,7 @@ where **coverage** is the number of nucleotides divided by the total length of the provided intervals. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_thread_for_species.xml --- a/tools/maf/maf_thread_for_species.xml +++ b/tools/maf/maf_thread_for_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_Thread_For_Species1" name="Join MAF blocks"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_thread_for_species.py $input1 $out_file1 $species</command><inputs><param format="maf" name="input1" type="data" label="MAF file"/> @@ -48,13 +51,9 @@ s hg17.chr7 127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG s panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG ------- +@HELP_CITATIONS@ + </help> + <expand macro="citations" /> -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml +++ b/tools/maf/maf_to_bed.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_BED1" name="MAF to BED" force_history_refresh="True"><description>Converts a MAF formatted file to the BED format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_to_bed.py "${ input1 }" "${ out_file1 }" "${ species }" "${ complete_blocks }" "." "${ out_file1.id }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/> @@ -123,14 +126,9 @@ 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /><code file="maf_to_bed_code.py"/></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml +++ b/tools/maf/maf_to_fasta.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1"><description>Converts a MAF formatted file to FASTA format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks #else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1 @@ -188,12 +191,7 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml +++ b/tools/maf/maf_to_interval.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"><description>Converts a MAF formatted file to the Interval format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_to_interval.py "${ input1 }" "${ out_file1 }" "${ out_file1.id }" "." "${ input1.dbkey }" "${ species }" "${ input1.metadata.species }" "${ complete_blocks }" "${ remove_gaps }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/> @@ -121,13 +124,8 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/maf/vcf_to_maf_customtrack.xml --- a/tools/maf/vcf_to_maf_customtrack.xml +++ b/tools/maf/vcf_to_maf_customtrack.xml @@ -1,5 +1,8 @@ <tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track"><description>for display at UCSC</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">vcf_to_maf_customtrack.py '$out_file1' #if $vcf_source_type.vcf_file '${vcf_source_type.vcf_file[0].vcf_input.dbkey}' @@ -121,12 +124,8 @@ s CHB+JPT_1.5 0 1 + 1 *------ s CHB+JPT_2.5 0 7 + 7 *GGA*** ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/beam.xml --- a/tools/phenotype_association/beam.xml +++ b/tools/phenotype_association/beam.xml @@ -134,4 +134,8 @@ Submitted. </help> + <citations> + <citation type="doi">10.1038/ng2110</citation> + <citation type="doi">10.1214/11-AOAS469</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/gpass.xml --- a/tools/phenotype_association/gpass.xml +++ b/tools/phenotype_association/gpass.xml @@ -109,4 +109,7 @@ Submitted. </help> + <citations> + <citation type="doi">10.1198/jasa.2011.ap10657</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/ldtools.xml --- a/tools/phenotype_association/ldtools.xml +++ b/tools/phenotype_association/ldtools.xml @@ -108,4 +108,7 @@ Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15. </help> + <citations> + <citation type="doi">10.1086/381000</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/linkToDavid.xml --- a/tools/phenotype_association/linkToDavid.xml +++ b/tools/phenotype_association/linkToDavid.xml @@ -107,4 +107,8 @@ Genome Biol. 4(5):P3. Epub 2003 Apr 3. </help> + <citations> + <citation type="doi">10.1038/nprot.2008.211</citation> + <citation type="doi">10.1186/gb-2003-4-5-p3</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/linkToGProfile.xml --- a/tools/phenotype_association/linkToGProfile.xml +++ b/tools/phenotype_association/linkToGProfile.xml @@ -87,4 +87,7 @@ Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3. </help> + <citations> + <citation type="doi">10.1093/nar/gkm226</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -301,4 +301,18 @@ --></help> + <citations> + <citation type="bibtex">@ARTICLE{Kim07aninterior-point, + author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky}, + title = {An interior-point method for large-scale l1-regularized logistic regression}, + journal = {Journal of Machine Learning Research}, + year = {2007}, + volume = {2007} +}</citation> + <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm, + author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein}, + title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, + year = {2008} +}</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/pass.xml --- a/tools/phenotype_association/pass.xml +++ b/tools/phenotype_association/pass.xml @@ -123,4 +123,8 @@ Submitted. </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btn549</citation> + <citation type="doi">10.1093/bioinformatics/btq379</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/phenotype_association/sift.xml --- a/tools/phenotype_association/sift.xml +++ b/tools/phenotype_association/sift.xml @@ -171,4 +171,10 @@ Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25. </help> + <citations> + <citation type="doi">10.1101/gr.176601</citation> + <citation type="doi">10.1101/gr.212802</citation> + <citation type="doi">10.1093/nar/gkg509</citation> + <citation type="doi">10.1038/nprot.2009.86</citation> + </citations></tool> diff -r 3ba68bb089e15a393724db39e2a2ed1d25d2f579 -r 08d1eb86cd6f9f519880bce2a17b651be2bc928a tools/plotting/boxplot.xml --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -105,4 +105,7 @@ </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.