1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/30ae36e55f86/
Changeset: 30ae36e55f86
User: guerler
Date: 2014-02-04 21:02:46
Summary: Upload: Change icon
Affected #: 2 files
diff -r e1ac3242786b055b8cc2b80ed701643f41c1e42e -r 30ae36e55f869920a7959cef0e166a00f0be3d2b static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -292,7 +292,7 @@
for (key in self.app.select_extension)
tmpl += '<option value="' + self.app.select_extension[key][1] + '">' + self.app.select_extension[key][0] + '</option>';
tmpl += '</select>' +
- ' <i id="extension_info" class="fa fa-question" style="cursor: pointer;"/>' +
+ ' <i id="extension_info" class="fa fa-search" style="cursor: pointer;"/>' +
'</td>';
// add genome selector
diff -r e1ac3242786b055b8cc2b80ed701643f41c1e42e -r 30ae36e55f869920a7959cef0e166a00f0be3d2b static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["mvc/upload/upload-model","mvc/upload/upload-extensions"],function(a,b){return Backbone.View.extend({options:{padding:8,timeout:2000},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",running:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(f,d){this.app=f;var c=this;this.model=new a.Model(d);this.setElement(this._template(d));var e=this.$el;e.find("#symbol").on("click",function(){var g=c.model.get("status");if(g=="init"||g=="success"||g=="error"){c.app.collection.remove(c.model)}});e.find("#extension_info").on("mouseover",function(){c._showExtensionInfo()}).on("mouseleave",function(){c._hideExtensionInfo()});e.find("#text-content").on("keyup",function(){var g=e.find("#text-content");var i=g.val();var h=i.length;e.find("#size").html(c._formatSize(h));c.model.set("url_paste",i);c.model.set("file_size",h)});e.find("#genome").on("change",function(g){c.model.set("genome",$(g.target).val())});e.find("#extension").on("change",function(g){c.model.set("extension",$(g.target).val());c.$el.find("#extension_info").popover("destroy")});e.find("#space_to_tabs").on("change",function(g){c.model.set("space_to_tabs",$(g.target).prop("checked"))});this.model.on("change:percentage",function(){c._refreshPercentage()});this.model.on("change:status",function(){c._refreshStatus()});this.model.on("change:info",function(){c._refreshInfo()});this.model.on("change:genome",function(){c._refreshGenome()});this.model.on("remove",function(){c.remove()});this.app.collection.on("reset",function(){c.remove()})},render:function(){var i=this.model.get("file_name");var d=this.model.get("file_size");var f=this.$el;f.find("#title").html(i);f.find("#size").html(this._formatSize(d));if(d==-1){var h=f.find("#text");var g=this.options.padding;var e=f.width()-2*g;var c=f.height()-g;h.css("width",e+"px");h.css("top",c+"px");f.height(c+h.height()+2*g);h.show()}},_refreshGenome:function(){var c=this.model.get("genome");this.$el.find("#genome").val(c)},_refreshInfo:function(){var c=this.model.get("info");if(c){this.$el.find("#info").html("<strong>Failed: </strong>"+c).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var c=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:c+"%"});if(c!=100){this.$el.find("#percentage").html(c+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var d=this.$el;var c=this.model.get("status");var f=this.status_classes[c];var e=this.$el.find("#symbol");e.removeClass();e.addClass(f);if(c=="init"){d.find("#text-content").attr("disabled",false);d.find("#genome").attr("disabled",false);d.find("#extension").attr("disabled",false);d.find("#space_to_tabs").attr("disabled",false)}else{d.find("#text-content").attr("disabled",true);d.find("#genome").attr("disabled",true);d.find("#extension").attr("disabled",true);d.find("#space_to_tabs").attr("disabled",true)}if(c=="success"){d.addClass("success");d.find("#percentage").html("100%")}if(c=="error"){d.addClass("danger");d.find(".progress").remove()}},_formatSize:function(c){var d="";if(c>=100000000000){c=c/100000000000;d="TB"}else{if(c>=100000000){c=c/100000000;d="GB"}else{if(c>=100000){c=c/100000;d="MB"}else{if(c>=100){c=c/100;d="KB"}else{if(c>0){c=c*10;d="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(c)/10)+"</strong> "+d},_showExtensionInfo:function(){var c=this;var d=$(this.el).find("#extension_info");var f=this.model.get("extension");var e=$(this.el).find("#extension").find("option:selected").text();d.popover({html:true,title:e,content:b(f),placement:"bottom",container:c.$el.parent()});d.popover("show");clearTimeout(this.popover_timeout)},_hideExtensionInfo:function(){var c=this;this.popover_timeout=setTimeout(function(){c.$el.find("#extension_info").popover("destroy")},this.options.timeout)},_template:function(e){var d=this;var c='<tr id="upload-item-'+e.id+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';c+='<td><select id="extension" class="extension">';for(key in d.app.select_extension){c+='<option value="'+d.app.select_extension[key][1]+'">'+d.app.select_extension[key][0]+"</option>"}c+='</select> <i id="extension_info" class="fa fa-question" style="cursor: pointer;"/></td>';c+='<td><select id="genome" class="genome">';for(key in d.app.select_genome){c+='<option value="'+d.app.select_genome[key][1]+'">'+d.app.select_genome[key][0]+"</option>"}c+="</select></td>";c+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return c}})});
\ No newline at end of file
+define(["mvc/upload/upload-model","mvc/upload/upload-extensions"],function(a,b){return Backbone.View.extend({options:{padding:8,timeout:2000},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",running:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(f,d){this.app=f;var c=this;this.model=new a.Model(d);this.setElement(this._template(d));var e=this.$el;e.find("#symbol").on("click",function(){var g=c.model.get("status");if(g=="init"||g=="success"||g=="error"){c.app.collection.remove(c.model)}});e.find("#extension_info").on("mouseover",function(){c._showExtensionInfo()}).on("mouseleave",function(){c._hideExtensionInfo()});e.find("#text-content").on("keyup",function(){var g=e.find("#text-content");var i=g.val();var h=i.length;e.find("#size").html(c._formatSize(h));c.model.set("url_paste",i);c.model.set("file_size",h)});e.find("#genome").on("change",function(g){c.model.set("genome",$(g.target).val())});e.find("#extension").on("change",function(g){c.model.set("extension",$(g.target).val());c.$el.find("#extension_info").popover("destroy")});e.find("#space_to_tabs").on("change",function(g){c.model.set("space_to_tabs",$(g.target).prop("checked"))});this.model.on("change:percentage",function(){c._refreshPercentage()});this.model.on("change:status",function(){c._refreshStatus()});this.model.on("change:info",function(){c._refreshInfo()});this.model.on("change:genome",function(){c._refreshGenome()});this.model.on("remove",function(){c.remove()});this.app.collection.on("reset",function(){c.remove()})},render:function(){var i=this.model.get("file_name");var d=this.model.get("file_size");var f=this.$el;f.find("#title").html(i);f.find("#size").html(this._formatSize(d));if(d==-1){var h=f.find("#text");var g=this.options.padding;var e=f.width()-2*g;var c=f.height()-g;h.css("width",e+"px");h.css("top",c+"px");f.height(c+h.height()+2*g);h.show()}},_refreshGenome:function(){var c=this.model.get("genome");this.$el.find("#genome").val(c)},_refreshInfo:function(){var c=this.model.get("info");if(c){this.$el.find("#info").html("<strong>Failed: </strong>"+c).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var c=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:c+"%"});if(c!=100){this.$el.find("#percentage").html(c+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var d=this.$el;var c=this.model.get("status");var f=this.status_classes[c];var e=this.$el.find("#symbol");e.removeClass();e.addClass(f);if(c=="init"){d.find("#text-content").attr("disabled",false);d.find("#genome").attr("disabled",false);d.find("#extension").attr("disabled",false);d.find("#space_to_tabs").attr("disabled",false)}else{d.find("#text-content").attr("disabled",true);d.find("#genome").attr("disabled",true);d.find("#extension").attr("disabled",true);d.find("#space_to_tabs").attr("disabled",true)}if(c=="success"){d.addClass("success");d.find("#percentage").html("100%")}if(c=="error"){d.addClass("danger");d.find(".progress").remove()}},_formatSize:function(c){var d="";if(c>=100000000000){c=c/100000000000;d="TB"}else{if(c>=100000000){c=c/100000000;d="GB"}else{if(c>=100000){c=c/100000;d="MB"}else{if(c>=100){c=c/100;d="KB"}else{if(c>0){c=c*10;d="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(c)/10)+"</strong> "+d},_showExtensionInfo:function(){var c=this;var d=$(this.el).find("#extension_info");var f=this.model.get("extension");var e=$(this.el).find("#extension").find("option:selected").text();d.popover({html:true,title:e,content:b(f),placement:"bottom",container:c.$el.parent()});d.popover("show");clearTimeout(this.popover_timeout)},_hideExtensionInfo:function(){var c=this;this.popover_timeout=setTimeout(function(){c.$el.find("#extension_info").popover("destroy")},this.options.timeout)},_template:function(e){var d=this;var c='<tr id="upload-item-'+e.id+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';c+='<td><select id="extension" class="extension">';for(key in d.app.select_extension){c+='<option value="'+d.app.select_extension[key][1]+'">'+d.app.select_extension[key][0]+"</option>"}c+='</select> <i id="extension_info" class="fa fa-search" style="cursor: pointer;"/></td>';c+='<td><select id="genome" class="genome">';for(key in d.app.select_genome){c+='<option value="'+d.app.select_genome[key][1]+'">'+d.app.select_genome[key][0]+"</option>"}c+="</select></td>";c+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return c}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e1ac3242786b/
Changeset: e1ac3242786b
User: guerler
Date: 2014-02-04 20:53:26
Summary: Upload: Add file extension descriptions
Affected #: 8 files
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/mvc/upload/upload-extensions.js
--- /dev/null
+++ b/static/scripts/mvc/upload/upload-extensions.js
@@ -0,0 +1,110 @@
+// dependencies
+define([], function() {
+
+var dictionary = {
+
+ auto : {
+ text: 'The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed'
+ },
+
+ ab1 : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Ab1',
+ text: 'A binary sequence file in \'ab1\' format with a \'.ab1\' file extension. You must manually select this \'File Format\' when uploading the file.'
+ },
+
+ axt : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Axt',
+ text: 'blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields.'
+ },
+
+ bam : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#BAM',
+ text: 'A binary file compressed in the BGZF format with a \'.bam\' file extension.'
+ },
+
+ bed : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Bed',
+ text: 'BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd.'
+ },
+
+ fasta : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Fasta',
+ text: 'A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters.'
+ },
+
+ fastq : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Fastq',
+ text: 'FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. '
+ },
+
+ fastqsolexa : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa',
+ text: 'FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file.'
+ },
+
+ gff : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF',
+ text: 'GFF lines have nine required fields that must be tab-separated.'
+ },
+
+ gff3 : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3',
+ text: 'The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.'
+ },
+
+ interval : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3',
+ text: 'File must start with definition line in the following format (columns may be in any order).'
+ },
+
+ lav : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3',
+ text: 'Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav..'
+ },
+
+ maf : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#MAF',
+ text: 'TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=".'
+ },
+
+ scf : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Scf',
+ text: 'A binary sequence file in \'scf\' format with a \'.scf\' file extension. You must manually select this \'File Format\' when uploading the file.'
+ },
+
+ sff : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Sff',
+ text: 'A binary file in \'Standard Flowgram Format\' with a \'.sff\' file extension.'
+ },
+
+ tabular : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29',
+ text: 'Any data in tab delimited format (tabular).'
+ },
+
+ wig : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Wig',
+ text: 'The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track.'
+ },
+
+ txt : {
+ url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text',
+ text: 'Any text file.'
+ },
+
+};
+
+// create description content
+return function(key) {
+ var description = dictionary[key];
+ if (description) {
+ var tmpl = description.text;
+ if (description.url) {
+ tmpl += ' (<a href="' + description.url + '" target="_blank">read more</a>)';
+ }
+ return tmpl;
+ } else {
+ return 'There is no description available for this file extension.';
+ }
+}
+});
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/mvc/upload/upload-row.js
--- a/static/scripts/mvc/upload/upload-row.js
+++ b/static/scripts/mvc/upload/upload-row.js
@@ -1,11 +1,12 @@
// dependencies
-define(['mvc/upload/upload-model'], function(UploadModel) {
+define(['mvc/upload/upload-model', 'mvc/upload/upload-extensions'], function(UploadModel, UploadExtensions) {
// item view
return Backbone.View.extend({
// options
options: {
- padding : 8
+ padding : 8,
+ timeout : 2000
},
// states
@@ -46,6 +47,10 @@
self.app.collection.remove(self.model);
}
});
+
+ // handle mouse over
+ it.find('#extension_info').on('mouseover' , function() { self._showExtensionInfo(); })
+ .on('mouseleave', function() { self._hideExtensionInfo(); });
// handle text editing event
it.find('#text-content').on('keyup', function() {
@@ -70,6 +75,7 @@
// handle extension selection
it.find('#extension').on('change', function(e) {
self.model.set('extension', $(e.target).val());
+ self.$el.find('#extension_info').popover('destroy');
});
// handle space to tabs button
@@ -139,7 +145,7 @@
// genome
_refreshGenome: function()
{
- // write error message
+ // update genome info on screen
var genome = this.model.get('genome');
this.$el.find('#genome').val(genome);
},
@@ -226,6 +232,41 @@
return '<strong>' + (Math.round(size) / 10) + '</strong> ' + unit;
},
+ // attach file info popup
+ _showExtensionInfo : function()
+ {
+ // initialize
+ var self = this;
+ var $el = $(this.el).find('#extension_info');
+ var extension = this.model.get('extension');
+ var title = $(this.el).find('#extension').find('option:selected').text();
+
+ // create popup
+ $el.popover({
+ html: true,
+ title: title,
+ content: UploadExtensions(extension),
+ placement: 'bottom',
+ container: self.$el.parent()
+ });
+
+ // show popup
+ $el.popover('show');
+
+ // clear previous timers
+ clearTimeout(this.popover_timeout);
+ },
+
+ // attach file info popup
+ _hideExtensionInfo : function()
+ {
+ // remove popup
+ var self = this
+ this.popover_timeout = setTimeout(function() {
+ self.$el.find('#extension_info').popover('destroy');
+ }, this.options.timeout);
+ },
+
// template
_template: function(options)
{
@@ -251,6 +292,7 @@
for (key in self.app.select_extension)
tmpl += '<option value="' + self.app.select_extension[key][1] + '">' + self.app.select_extension[key][0] + '</option>';
tmpl += '</select>' +
+ ' <i id="extension_info" class="fa fa-question" style="cursor: pointer;"/>' +
'</td>';
// add genome selector
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/packed/mvc/upload/upload-extensions.js
--- /dev/null
+++ b/static/scripts/packed/mvc/upload/upload-extensions.js
@@ -0,0 +1,1 @@
+define([],function(){var a={auto:{text:"The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed"},ab1:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Ab1",text:"A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file."},axt:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Axt",text:"blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields."},bam:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#BAM",text:"A binary file compressed in the BGZF format with a '.bam' file extension."},bed:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Bed",text:"BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd."},fasta:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Fasta",text:'A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters.'},fastq:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Fastq",text:"FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. "},fastqsolexa:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa",text:"FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file."},gff:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF",text:"GFF lines have nine required fields that must be tab-separated."},gff3:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats."},interval:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"File must start with definition line in the following format (columns may be in any order)."},lav:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.."},maf:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#MAF",text:'TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=".'},scf:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Scf",text:"A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file."},sff:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Sff",text:"A binary file in 'Standard Flowgram Format' with a '.sff' file extension."},tabular:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29",text:"Any data in tab delimited format (tabular)."},wig:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Wig",text:"The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track."},txt:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text",text:"Any text file."},};return function(c){var d=a[c];if(d){var b=d.text;if(d.url){b+=' (<a href="'+d.url+'" target="_blank">read more</a>)'}return b}else{return"There is no description available for this file extension."}}});
\ No newline at end of file
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/packed/mvc/upload/upload-row.js
--- a/static/scripts/packed/mvc/upload/upload-row.js
+++ b/static/scripts/packed/mvc/upload/upload-row.js
@@ -1,1 +1,1 @@
-define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",running:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h);b.model.set("file_size",g)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("<strong>Failed: </strong>"+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(b)/10)+"</strong> "+c},_template:function(d){var c=this;var b='<tr id="upload-item-'+d.id+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';b+='<td><select id="extension" class="extension">';for(key in c.app.select_extension){b+='<option value="'+c.app.select_extension[key][1]+'">'+c.app.select_extension[key][0]+"</option>"}b+="</select></td>";b+='<td><select id="genome" class="genome">';for(key in c.app.select_genome){b+='<option value="'+c.app.select_genome[key][1]+'">'+c.app.select_genome[key][0]+"</option>"}b+="</select></td>";b+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return b}})});
\ No newline at end of file
+define(["mvc/upload/upload-model","mvc/upload/upload-extensions"],function(a,b){return Backbone.View.extend({options:{padding:8,timeout:2000},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",running:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(f,d){this.app=f;var c=this;this.model=new a.Model(d);this.setElement(this._template(d));var e=this.$el;e.find("#symbol").on("click",function(){var g=c.model.get("status");if(g=="init"||g=="success"||g=="error"){c.app.collection.remove(c.model)}});e.find("#extension_info").on("mouseover",function(){c._showExtensionInfo()}).on("mouseleave",function(){c._hideExtensionInfo()});e.find("#text-content").on("keyup",function(){var g=e.find("#text-content");var i=g.val();var h=i.length;e.find("#size").html(c._formatSize(h));c.model.set("url_paste",i);c.model.set("file_size",h)});e.find("#genome").on("change",function(g){c.model.set("genome",$(g.target).val())});e.find("#extension").on("change",function(g){c.model.set("extension",$(g.target).val());c.$el.find("#extension_info").popover("destroy")});e.find("#space_to_tabs").on("change",function(g){c.model.set("space_to_tabs",$(g.target).prop("checked"))});this.model.on("change:percentage",function(){c._refreshPercentage()});this.model.on("change:status",function(){c._refreshStatus()});this.model.on("change:info",function(){c._refreshInfo()});this.model.on("change:genome",function(){c._refreshGenome()});this.model.on("remove",function(){c.remove()});this.app.collection.on("reset",function(){c.remove()})},render:function(){var i=this.model.get("file_name");var d=this.model.get("file_size");var f=this.$el;f.find("#title").html(i);f.find("#size").html(this._formatSize(d));if(d==-1){var h=f.find("#text");var g=this.options.padding;var e=f.width()-2*g;var c=f.height()-g;h.css("width",e+"px");h.css("top",c+"px");f.height(c+h.height()+2*g);h.show()}},_refreshGenome:function(){var c=this.model.get("genome");this.$el.find("#genome").val(c)},_refreshInfo:function(){var c=this.model.get("info");if(c){this.$el.find("#info").html("<strong>Failed: </strong>"+c).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var c=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:c+"%"});if(c!=100){this.$el.find("#percentage").html(c+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var d=this.$el;var c=this.model.get("status");var f=this.status_classes[c];var e=this.$el.find("#symbol");e.removeClass();e.addClass(f);if(c=="init"){d.find("#text-content").attr("disabled",false);d.find("#genome").attr("disabled",false);d.find("#extension").attr("disabled",false);d.find("#space_to_tabs").attr("disabled",false)}else{d.find("#text-content").attr("disabled",true);d.find("#genome").attr("disabled",true);d.find("#extension").attr("disabled",true);d.find("#space_to_tabs").attr("disabled",true)}if(c=="success"){d.addClass("success");d.find("#percentage").html("100%")}if(c=="error"){d.addClass("danger");d.find(".progress").remove()}},_formatSize:function(c){var d="";if(c>=100000000000){c=c/100000000000;d="TB"}else{if(c>=100000000){c=c/100000000;d="GB"}else{if(c>=100000){c=c/100000;d="MB"}else{if(c>=100){c=c/100;d="KB"}else{if(c>0){c=c*10;d="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(c)/10)+"</strong> "+d},_showExtensionInfo:function(){var c=this;var d=$(this.el).find("#extension_info");var f=this.model.get("extension");var e=$(this.el).find("#extension").find("option:selected").text();d.popover({html:true,title:e,content:b(f),placement:"bottom",container:c.$el.parent()});d.popover("show");clearTimeout(this.popover_timeout)},_hideExtensionInfo:function(){var c=this;this.popover_timeout=setTimeout(function(){c.$el.find("#extension_info").popover("destroy")},this.options.timeout)},_template:function(e){var d=this;var c='<tr id="upload-item-'+e.id+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';c+='<td><select id="extension" class="extension">';for(key in d.app.select_extension){c+='<option value="'+d.app.select_extension[key][1]+'">'+d.app.select_extension[key][0]+"</option>"}c+='</select> <i id="extension_info" class="fa fa-question" style="cursor: pointer;"/></td>';c+='<td><select id="genome" class="genome">';for(key in d.app.select_genome){c+='<option value="'+d.app.select_genome[key][1]+'">'+d.app.select_genome[key][0]+"</option>"}c+="</select></td>";c+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return c}})});
\ No newline at end of file
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/packed/utils/uploadbox.js
--- a/static/scripts/packed/utils/uploadbox.js
+++ b/static/scripts/packed/utils/uploadbox.js
@@ -1,1 +1,1 @@
-(function(c){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:2048,maxfilenumber:20,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(k,l,m){alert(m)},complete:function(){},error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in.",error_missing:"No upload content available."};var a={};var e={};var f=0;var j=0;var d=false;var g=false;var b=null;var i=null;c.fn.uploadbox=function(A){a=c.extend({},h,A);b=this;b.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');b.on("drop",o);b.on("dragover",p);b.on("dragleave",x);c("#uploadbox_input").change(function(B){z(B.target.files);c(this).val("")});function o(B){if(!B.dataTransfer){return}z(B.dataTransfer.files);B.preventDefault();return false}function p(B){B.preventDefault();a.dragover.call(B)}function x(B){B.stopPropagation();a.dragleave.call(B)}function k(B){if(B.lengthComputable){a.progress(this.index,this.file,Math.round((B.loaded*100)/B.total))}}function z(D){if(d){return}for(var C=0;C<D.length;C++){if(j>=a.maxfilenumber){break}var B=String(f++);e[B]=D[C];a.announce(B,e[B],"");j++}}function r(B){if(e[B]){delete e[B];j--}}function m(){if(j==0||g){g=false;d=false;a.complete();return}else{d=true}var D=-1;for(var F in e){D=F;break}var E=e[D];r(D);var C=E.size;var B=1048576*a.maxfilesize;if(C<B){var G=a.initialize(D,E);if(G){q(D,E,G)}else{u(D,E,a.error_missing)}}else{u(D,E,a.error_filesize)}}function q(B,D,E){var F=new FormData();for(var C in E){F.append(C,E[C])}if(D.size>0){F.append(a.paramname,D,D.name)}i=new XMLHttpRequest();i.open("POST",a.url,true);i.setRequestHeader("Accept","application/json");i.setRequestHeader("Cache-Control","no-cache");i.setRequestHeader("X-Requested-With","XMLHttpRequest");i.onreadystatechange=function(){if(i.readyState!=i.DONE){return}var G=null;if(i.responseText){try{G=jQuery.parseJSON(i.responseText)}catch(H){G=i.responseText}}if(i.status<200||i.status>299){var I=i.statusText;if(i.status==403){I=a.error_login}else{if(i.status==0){I=a.error_server}else{if(!I){I=a.error_default}}}u(B,D,I+" ("+i.status+")")}else{y(B,D,G)}};i.upload.index=B;i.upload.file=D;i.upload.addEventListener("progress",k,false);i.send(F)}function y(B,C,D){a.success(B,C,D);m()}function u(B,C,D){a.error(B,C,D);m()}function w(){c("#uploadbox_input").trigger("click")}function t(B){for(B in e){r(B)}}function l(){if(!d){d=true;m()}}function v(){g=true}function n(B){a=c.extend({},a,B);return a}function s(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:w,add:z,remove:r,start:l,stop:v,reset:t,configure:n,compatible:s}}})(jQuery);
\ No newline at end of file
+(function(c){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:2048,maxfilenumber:50,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(k,l,m){alert(m)},complete:function(){},error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in.",error_missing:"No upload content available."};var a={};var e={};var f=0;var j=0;var d=false;var g=false;var b=null;var i=null;c.fn.uploadbox=function(A){a=c.extend({},h,A);b=this;b.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');b.on("drop",o);b.on("dragover",p);b.on("dragleave",x);c("#uploadbox_input").change(function(B){z(B.target.files);c(this).val("")});function o(B){if(!B.dataTransfer){return}z(B.dataTransfer.files);B.preventDefault();return false}function p(B){B.preventDefault();a.dragover.call(B)}function x(B){B.stopPropagation();a.dragleave.call(B)}function k(B){if(B.lengthComputable){a.progress(this.index,this.file,Math.round((B.loaded*100)/B.total))}}function z(D){if(d){return}for(var C=0;C<D.length;C++){if(j>=a.maxfilenumber){break}var B=String(f++);e[B]=D[C];a.announce(B,e[B],"");j++}}function r(B){if(e[B]){delete e[B];j--}}function m(){if(j==0||g){g=false;d=false;a.complete();return}else{d=true}var D=-1;for(var F in e){D=F;break}var E=e[D];r(D);var C=E.size;var B=1048576*a.maxfilesize;if(C<B){var G=a.initialize(D,E);if(G){q(D,E,G)}else{u(D,E,a.error_missing)}}else{u(D,E,a.error_filesize)}}function q(B,D,E){var F=new FormData();for(var C in E){F.append(C,E[C])}if(D.size>0){F.append(a.paramname,D,D.name)}i=new XMLHttpRequest();i.open("POST",a.url,true);i.setRequestHeader("Accept","application/json");i.setRequestHeader("Cache-Control","no-cache");i.setRequestHeader("X-Requested-With","XMLHttpRequest");i.onreadystatechange=function(){if(i.readyState!=i.DONE){return}var G=null;if(i.responseText){try{G=jQuery.parseJSON(i.responseText)}catch(H){G=i.responseText}}if(i.status<200||i.status>299){var I=i.statusText;if(i.status==403){I=a.error_login}else{if(i.status==0){I=a.error_server}else{if(!I){I=a.error_default}}}u(B,D,I+" ("+i.status+")")}else{y(B,D,G)}};i.upload.index=B;i.upload.file=D;i.upload.addEventListener("progress",k,false);i.send(F)}function y(B,C,D){a.success(B,C,D);m()}function u(B,C,D){a.error(B,C,D);m()}function w(){c("#uploadbox_input").trigger("click")}function t(B){for(B in e){r(B)}}function l(){if(!d){d=true;m()}}function v(){g=true}function n(B){a=c.extend({},a,B);return a}function s(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:w,add:z,remove:r,start:l,stop:v,reset:t,configure:n,compatible:s}}})(jQuery);
\ No newline at end of file
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/scripts/utils/uploadbox.js
--- a/static/scripts/utils/uploadbox.js
+++ b/static/scripts/utils/uploadbox.js
@@ -12,7 +12,7 @@
url : '',
paramname : 'content',
maxfilesize : 2048,
- maxfilenumber : 20,
+ maxfilenumber : 50,
dragover : function() {},
dragleave : function() {},
announce : function() {},
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1257,7 +1257,8 @@
.progress-button .progress-bar-notransition{-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none}
.progress-button .label{position:absolute;top:0px;width:inherit;text-align:center;line-height:19px}
.upload-info{font-weight:normal;text-align:center}
-.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%}
+.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .popover{max-width:600px;width:auto}
+.upload-box .table{width:100%}
.upload-box .table th{text-align:center;white-space:nowrap}
.upload-box .table td{margin:0px;paddign:0px}
.upload-box .title{width:130px;word-wrap:break-word;font-size:11px}
diff -r 82d2c2109792d098ddc5ede7992ae132e596584a -r e1ac3242786b055b8cc2b80ed701643f41c1e42e static/style/src/less/upload.less
--- a/static/style/src/less/upload.less
+++ b/static/style/src/less/upload.less
@@ -61,7 +61,12 @@
padding : 10px;
overflow-x : hidden;
-ms-overflow-style: none;
-
+
+ .popover {
+ max-width: 500px;
+ width: auto;
+ }
+
.table {
width : 100%;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c043a2ca8051/
Changeset: c043a2ca8051
User: guerler
Date: 2014-02-03 22:23:53
Summary: Grids: Fix filter column separator
Affected #: 1 file
diff -r 519797105a694ac9044e5e6139380a51c5c5fc52 -r c043a2ca8051de612d4e895ba55e6dce0697a8d3 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -132,7 +132,7 @@
if len( column_filter ) == 1:
column_filter = column_filter[0]
# Interpret ',' as a separator for multiple terms.
- elif isinstance( column_filter, basestring ) and column_filter.find(',') != -1:
+ if isinstance( column_filter, basestring ) and column_filter.find(',') != -1:
column_filter = column_filter.split(',')
# Check if filter is empty
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/37544732f61c/
Changeset: 37544732f61c
User: jmchilton
Date: 2014-02-03 17:11:31
Summary: Improve examples of newer tool functional test features.
Affected #: 3 files
diff -r 0f636b29e4f58d1568e8658dcae57e3c45a14563 -r 37544732f61c32202d134c263c1257f0920e36a0 test/functional/tools/README.txt
--- a/test/functional/tools/README.txt
+++ b/test/functional/tools/README.txt
@@ -1,3 +1,3 @@
This directory contains tools only useful for testing the tool test framework
and demonstrating it features. Run the driver script 'run_functional_tests.sh'
-with '-installed' as first argument to run through these tests.
+with '-framework' as first argument to run through these tests.
diff -r 0f636b29e4f58d1568e8658dcae57e3c45a14563 -r 37544732f61c32202d134c263c1257f0920e36a0 test/functional/tools/disambiguate_cond.xml
--- a/test/functional/tools/disambiguate_cond.xml
+++ b/test/functional/tools/disambiguate_cond.xml
@@ -46,19 +46,8 @@
<data name="out_file1" format="txt" /></outputs><tests>
- <test>
- <param name="p1|use" value="True"/>
- <param name="p2|use" value="False"/>
- <param name="p3|use" value="True"/>
- <param name="p4|use" value="True" />
- <param name="p4|file" value="simple_line.txt" />
- <output name="out_file1">
- <assert_contents>
- <has_line line="4 7 4" />
- <has_line line="This is a line of text." />
- </assert_contents>
- </output>
- </test>
+ <!-- Can use nested conditional blocks as shown below to disambiguate
+ various nested parameters. --><test><conditional name="p1"><param name="use" value="False"/>
@@ -83,5 +72,23 @@
</assert_contents></output></test>
+ <!-- Can also use a more concise, flat verison of this, but it the
+ above version is more clear and should be considered preferable.
+ -->
+ <test>
+ <param name="p1|use" value="True"/>
+ <param name="p2|use" value="False"/>
+ <param name="p3|use" value="True"/>
+ <param name="p4|use" value="True" />
+ <!-- Only need to specify enough of a suffix to disambiguate,
+ but don't do this - it is too clever. -->
+ <param name="p4|file" value="simple_line.txt" />
+ <output name="out_file1">
+ <assert_contents>
+ <has_line line="4 7 4" />
+ <has_line line="This is a line of text." />
+ </assert_contents>
+ </output>
+ </test></tests></tool>
diff -r 0f636b29e4f58d1568e8658dcae57e3c45a14563 -r 37544732f61c32202d134c263c1257f0920e36a0 test/functional/tools/disambiguate_repeats.xml
--- a/test/functional/tools/disambiguate_repeats.xml
+++ b/test/functional/tools/disambiguate_repeats.xml
@@ -14,17 +14,24 @@
<data name="out_file1" format="txt" /></outputs><tests>
- <!-- Can use prefixes to disambiguate inputs or force order. -->
+ <!-- Can disambiguate repeats and specify multiple blocks using,
+ nested structure. --><test>
- <param name="queries_1|input" value="simple_line_alternative.txt"/>
- <param name="queries_0|input" value="simple_line.txt"/>
-
- <param name="more_queries_1|input" value="simple_line_alternative.txt" />
- <param name="more_queries_0|input" value="simple_line.txt"/>
-
- <output name="out_file1" file="simple_lines_interleaved.txt"/>
+ <repeat name="queries">
+ <param name="input" value="simple_line.txt"/>
+ </repeat>
+ <repeat name="more_queries">
+ <param name="input" value="simple_line_alternative.txt"/>
+ </repeat>
+ <output name="out_file1">
+ <assert_contents>
+ <has_line line="This is a line of text." />
+ <has_line line="This is a different line of text." />
+ </assert_contents>
+ </output></test>
-
+ <!-- Multiple such blocks can be specified but only with newer API
+ driven tests. --><test><repeat name="queries"><param name="input" value="simple_line.txt"/>
@@ -40,6 +47,17 @@
</repeat><output name="out_file1" file="simple_lines_interleaved.txt"/></test>
+ <!-- Can also use prefixes to disambiguate inputs or force order, but
+ the above nested structure is preferable. -->
+ <test>
+ <param name="queries_1|input" value="simple_line_alternative.txt"/>
+ <param name="queries_0|input" value="simple_line.txt"/>
+
+ <param name="more_queries_1|input" value="simple_line_alternative.txt" />
+ <param name="more_queries_0|input" value="simple_line.txt"/>
+
+ <output name="out_file1" file="simple_lines_interleaved.txt"/>
+ </test></tests></tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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