mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000
This commit is contained in:
guerler
@@ -208,6 +208,7 @@ var View = Backbone.View.extend({
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if (this.options.searchable) {
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this.$select.select2('destroy');
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this.$select.select2();
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this.$( '.select2-container .select2-search input' ).off( 'blur' );
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}
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// set previous value
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@@ -32,16 +32,19 @@ module.exports = function( grunt ){
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'history-buttons': {
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src: fmt( '%s/history-buttons/*.png', imagesPath ),
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destImg: fmt( '%s/sprite-history-buttons.png', styleDistPath ),
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imgPath: fmt( 'sprite-history-buttons.png' ),
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destCSS: fmt( '%s/sprite-history-buttons.less', lessPath )
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},
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'history-states': {
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src: fmt( '%s/history-states/*.png', imagesPath ),
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destImg: fmt( '%s/sprite-history-states.png', styleDistPath ),
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imgPath: fmt( 'sprite-history-states.png' ),
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destCSS: fmt( '%s/sprite-history-states.less', lessPath )
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},
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'fugue': {
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src: fmt( '%s/fugue/*.png', imagesPath ),
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destImg: fmt( '%s/sprite-fugue.png', styleDistPath ),
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imgPath: fmt( 'sprite-fugue.png' ),
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destCSS: fmt( '%s/sprite-fugue.less', lessPath )
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}
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});
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@@ -350,8 +350,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
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# If your SMTP server requires SSL from the beginning of the connection
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# smtp_ssl = False
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# On the user registration form, users may choose to join the mailing list.
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# This is the address of the list they'll be subscribed to.
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# On the user registration form, users may choose to join a mailing list. This
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# is the address used to subscribe to the list. Uncomment and leave empty if you
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# want to remove this option from the user registration form.
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#mailing_join_addr = galaxy-announce-join@bx.psu.edu
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# Datasets in an error state include a link to report the error. Those reports
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@@ -585,8 +585,8 @@ class WorkflowContentsManager(UsesAnnotations):
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yield step_dict
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def __module_from_dict( self, trans, step_dict, secure ):
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""" Create a WorkflowStep model object and corrsponding module representing
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type-specific functionality from the incoming dicitionary.
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""" Create a WorkflowStep model object and corresponding module
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representing type-specific functionality from the incoming dictionary.
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"""
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step = model.WorkflowStep()
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# TODO: Consider handling position inside module.
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+53
-30
@@ -71,9 +71,8 @@ class ToolTestBuilder( object ):
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# No explicit value for param in test case, determine from default
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query_value = test_param.checked
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else:
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# Test case supplied value, check cases against this.
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query_value = string_as_bool( declared_value )
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matches_declared_value = lambda case_value: string_as_bool(case_value) == query_value
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query_value = _process_bool_param_value( test_param, declared_value )
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matches_declared_value = lambda case_value: _process_bool_param_value( test_param, case_value ) == query_value
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elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
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if declared_value is not None:
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# Test case supplied explicit value to check against.
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@@ -166,7 +165,8 @@ class ToolTestBuilder( object ):
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# as a new instance with value defined and hence enter
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# an infinite loop - hence the "case_value is not None"
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# check.
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expanded_inputs[ case_context.for_state() ] = expanded_case_value
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processed_value = _process_simple_value( value.test_param, expanded_case_value )
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expanded_inputs[ case_context.for_state() ] = processed_value
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elif isinstance( value, galaxy.tools.parameters.grouping.Section ):
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context = ParamContext( name=value.name, parent_context=parent_context )
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for r_name, r_value in value.inputs.iteritems():
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@@ -203,33 +203,8 @@ class ToolTestBuilder( object ):
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for ( name, value, extra ) in collection_def.collect_inputs():
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require_file( name, value, extra, self.required_files )
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processed_value = collection_def
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elif isinstance( value, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( value, 'static_options' ):
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# Tests may specify values as either raw value or the value
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# as they appear in the list - the API doesn't and shouldn't
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# accept the text value - so we need to convert the text
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# into the form value.
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def process_param_value( param_value ):
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found_value = False
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value_for_text = None
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if value.static_options:
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for (text, opt_value, selected) in value.static_options:
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if param_value == opt_value:
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found_value = True
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if value_for_text is None and param_value == text:
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value_for_text = opt_value
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if not found_value and value_for_text is not None:
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processed_value = value_for_text
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else:
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processed_value = param_value
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return processed_value
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# Do replacement described above for lists or singleton
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# values.
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if isinstance( param_value, list ):
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processed_value = map( process_param_value, param_value )
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else:
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processed_value = process_param_value( param_value )
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else:
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processed_value = param_value
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processed_value = _process_simple_value( value, param_value )
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expanded_inputs[ context.for_state() ] = processed_value
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return expanded_inputs
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@@ -240,6 +215,54 @@ class ToolTestBuilder( object ):
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return require_file( name, value, extra, self.required_files )
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def _process_simple_value( param, param_value ):
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if isinstance( param, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( param, 'static_options' ):
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# Tests may specify values as either raw value or the value
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# as they appear in the list - the API doesn't and shouldn't
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# accept the text value - so we need to convert the text
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||||
# into the form value.
|
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def process_param_value( param_value ):
|
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found_value = False
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value_for_text = None
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if param.static_options:
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for (text, opt_value, selected) in param.static_options:
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if param_value == opt_value:
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found_value = True
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if value_for_text is None and param_value == text:
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value_for_text = opt_value
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if not found_value and value_for_text is not None:
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processed_value = value_for_text
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else:
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processed_value = param_value
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return processed_value
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# Do replacement described above for lists or singleton
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# values.
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if isinstance( param_value, list ):
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processed_value = map( process_param_value, param_value )
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else:
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processed_value = process_param_value( param_value )
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elif isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter ):
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# Like above, tests may use the tool define values of simply
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# true/false.
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processed_value = _process_bool_param_value( param, param_value )
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else:
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processed_value = param_value
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return processed_value
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|
||||
|
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def _process_bool_param_value( param, param_value ):
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assert isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter )
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if isinstance( param_value, list ):
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param_value = param_value[0]
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if param.truevalue == param_value:
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processed_value = True
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elif param.falsevalue == param_value:
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processed_value = False
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else:
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||||
processed_value = string_as_bool( param_value )
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return processed_value
|
||||
|
||||
|
||||
@nottest
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||||
def test_data_iter( required_files ):
|
||||
for fname, extra in required_files:
|
||||
|
||||
@@ -1 +1 @@
|
||||
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|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-button-check"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.options.searchable&&(this.all_button=new b({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)),this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+a.label+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:c}});
|
||||
define(["utils/utils","mvc/ui/ui-button-check"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.options.searchable&&(this.all_button=new b({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)),this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2(),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+a.label+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:c}});
|
||||
//# sourceMappingURL=../../../maps/mvc/ui/ui-select-default.js.map
|
||||
+38
-38
@@ -2159,25 +2159,25 @@ div.historyItem .historyItemTitle{font-weight:bold;line-height:16px}
|
||||
.historyItemContainer:last-child div.historyItem{border-bottom:solid #bfbfbf 1px}
|
||||
div.historyItem div.historyItem{margin-right:-11px}
|
||||
div.historyItem-ok,div.historyItem-failed_metadata{background:#aff1af}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none}
|
||||
div.historyItem-error{background:#f9c7c5}div.historyItem-error .state-icon{background-image:url(../../../../../static/style/blue/sprite-history-states.png);background-position:0px -15px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-empty{background:#f9c7c5}div.historyItem-empty .state-icon{background-image:url(../../../../../static/style/blue/sprite-history-states.png);background-position:0px 0px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-error{background:#f9c7c5}div.historyItem-error .state-icon{background-image:url(sprite-history-states.png);background-position:0px -15px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-empty{background:#f9c7c5}div.historyItem-empty .state-icon{background-image:url(sprite-history-states.png);background-position:0px 0px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-running{background:#ffc}div.historyItem-running .state-icon{background-image:url(data_running.gif)}
|
||||
div.historyItem-setting_metadata{background:#ffc}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif)}
|
||||
div.historyItem-upload{background:#a6e4f7}div.historyItem-upload .state-icon{background-image:url(data_upload.gif)}
|
||||
div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(../../../../../static/style/blue/sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px}
|
||||
div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}div.historyItem-noPermission .state-icon{line-height:16px;display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-moz-osx-font-smoothing:grayscale;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-noPermission .state-icon:before{content:"\f05e"}
|
||||
div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-moz-osx-font-smoothing:grayscale;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-paused .state-icon:before{content:"\f04c"}
|
||||
div.historyItem-new .state-icon{line-height:16px;display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-moz-osx-font-smoothing:grayscale;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-new .state-icon:before{content:"\f071"}
|
||||
div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important}
|
||||
div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.display:hover{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.display_disabled{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete:hover{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete_disabled{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit:hover{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit_disabled{background-image:url(../../../../../static/style/blue/sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px}
|
||||
div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px}
|
||||
div.historyItemBody div{padding-top:2px}
|
||||
pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990}
|
||||
pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px}
|
||||
@@ -2349,30 +2349,30 @@ div.toolTitleNoSection{padding-bottom:5px;font-weight:bold}
|
||||
.btn-primary .text-and-autocomplete-select:after,.btn-success .text-and-autocomplete-select:after,.btn-warning .text-and-autocomplete-select:after,.btn-danger .text-and-autocomplete-select:after,.btn-info .text-and-autocomplete-select:after{border-top-color:#fff}
|
||||
.icon-button.general-question{background:url(question-octagon-frame.png) no-repeat;float:right;margin-top:3px;margin-right:4px}
|
||||
.icon-button.tag-question{background:url(question-balloon.png) no-repeat;float:right;margin-top:3px;margin-right:4px}
|
||||
.icon-button.tag{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -912px;width:16px;height:16px;height:16px}
|
||||
.icon-button.tags{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -928px;width:16px;height:16px;height:16px}
|
||||
.icon-button.tag--plus{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -896px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle-expand{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -976px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -944px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -992px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-circle{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -64px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -352px;width:16px;height:16px;height:16px}
|
||||
.icon-button.bug{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -288px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -496px;width:16px;height:16px;height:16px}
|
||||
.icon-button.information{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -656px;width:16px;height:16px;height:16px}
|
||||
.icon-button.annotate{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -880px;width:16px;height:16px;height:16px}
|
||||
.icon-button.go-to-full-screen{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px 0px;width:16px;height:16px;height:16px}
|
||||
.icon-button.import{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -864px;width:16px;height:16px;height:16px}
|
||||
.icon-button.plus-button{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -832px;width:16px;height:16px;height:16px}
|
||||
.icon-button.plus-button:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -848px;width:16px;height:16px;height:16px}
|
||||
.icon-button.gear{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -576px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chart_curve{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -304px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk--arrow{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -464px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk--arrow:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -480px;width:16px;height:16px;height:16px}
|
||||
.icon-button.cross-circle{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -400px;width:16px;height:16px;height:16px}
|
||||
.icon-button.cross-circle:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -416px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-split{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -112px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-split:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -128px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron-expand:hover{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -336px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron-expand{background-image:url(../../../../../static/style/blue/sprite-fugue.png);background-position:0px -320px;width:16px;height:16px;height:16px}
|
||||
.icon-button.tag{background-image:url(sprite-fugue.png);background-position:0px -912px;width:16px;height:16px;height:16px}
|
||||
.icon-button.tags{background-image:url(sprite-fugue.png);background-position:0px -928px;width:16px;height:16px;height:16px}
|
||||
.icon-button.tag--plus{background-image:url(sprite-fugue.png);background-position:0px -896px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle-expand{background-image:url(sprite-fugue.png);background-position:0px -976px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle{background-image:url(sprite-fugue.png);background-position:0px -944px;width:16px;height:16px;height:16px}
|
||||
.icon-button.toggle:hover{background-image:url(sprite-fugue.png);background-position:0px -992px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-circle{background-image:url(sprite-fugue.png);background-position:0px -64px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron{background-image:url(sprite-fugue.png);background-position:0px -352px;width:16px;height:16px;height:16px}
|
||||
.icon-button.bug{background-image:url(sprite-fugue.png);background-position:0px -288px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk{background-image:url(sprite-fugue.png);background-position:0px -496px;width:16px;height:16px;height:16px}
|
||||
.icon-button.information{background-image:url(sprite-fugue.png);background-position:0px -656px;width:16px;height:16px;height:16px}
|
||||
.icon-button.annotate{background-image:url(sprite-fugue.png);background-position:0px -880px;width:16px;height:16px;height:16px}
|
||||
.icon-button.go-to-full-screen{background-image:url(sprite-fugue.png);background-position:0px 0px;width:16px;height:16px;height:16px}
|
||||
.icon-button.import{background-image:url(sprite-fugue.png);background-position:0px -864px;width:16px;height:16px;height:16px}
|
||||
.icon-button.plus-button{background-image:url(sprite-fugue.png);background-position:0px -832px;width:16px;height:16px;height:16px}
|
||||
.icon-button.plus-button:hover{background-image:url(sprite-fugue.png);background-position:0px -848px;width:16px;height:16px;height:16px}
|
||||
.icon-button.gear{background-image:url(sprite-fugue.png);background-position:0px -576px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chart_curve{background-image:url(sprite-fugue.png);background-position:0px -304px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk--arrow{background-image:url(sprite-fugue.png);background-position:0px -464px;width:16px;height:16px;height:16px}
|
||||
.icon-button.disk--arrow:hover{background-image:url(sprite-fugue.png);background-position:0px -480px;width:16px;height:16px;height:16px}
|
||||
.icon-button.cross-circle{background-image:url(sprite-fugue.png);background-position:0px -400px;width:16px;height:16px;height:16px}
|
||||
.icon-button.cross-circle:hover{background-image:url(sprite-fugue.png);background-position:0px -416px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-split{background-image:url(sprite-fugue.png);background-position:0px -112px;width:16px;height:16px;height:16px}
|
||||
.icon-button.arrow-split:hover{background-image:url(sprite-fugue.png);background-position:0px -128px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron-expand:hover{background-image:url(sprite-fugue.png);background-position:0px -336px;width:16px;height:16px;height:16px}
|
||||
.icon-button.chevron-expand{background-image:url(sprite-fugue.png);background-position:0px -320px;width:16px;height:16px;height:16px}
|
||||
#for_bears{display:none}
|
||||
|
||||
@@ -2,6 +2,7 @@
|
||||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
||||
<head>
|
||||
<title>Homepage</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||||
<link rel="stylesheet" href="style/base.css" type="text/css" />
|
||||
</head>
|
||||
|
||||
@@ -152,7 +152,7 @@ def inherit(context):
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%if trans.app.config.smtp_server:
|
||||
%if trans.app.config.smtp_server and trans.app.config.mailing_join_addr:
|
||||
<div class="form-row">
|
||||
<label>Subscribe to mailing list:</label>
|
||||
%if subscribe_checked:
|
||||
|
||||
@@ -80,9 +80,9 @@
|
||||
else:
|
||||
user_email = ''
|
||||
%>
|
||||
<h2>Report this error to the Galaxy Team</h2>
|
||||
<h2>Report this error to the local Galaxy administrators</h2>
|
||||
<p>
|
||||
The Galaxy team regularly reviews errors that occur in the application.
|
||||
Usually the local Galaxy administrators regularly review errors that occur on the server.
|
||||
However, if you would like to provide additional information (such as
|
||||
what you were trying to do when the error occurred) and a contact e-mail
|
||||
address, we will be better able to investigate your problem and get back
|
||||
|
||||
@@ -0,0 +1,53 @@
|
||||
<tool id="boolean_conditional" name="boolean_conditional" version="1.0.0">
|
||||
<command>
|
||||
echo "$p1.p1val" >> $out_file1;
|
||||
</command>
|
||||
<inputs>
|
||||
<conditional name="p1">
|
||||
<param type="boolean" name="p1use" truevalue="booltrue" falsevalue="boolfalse" />
|
||||
<when value="booltrue">
|
||||
<param name="p1val" value="p1used" type="text" />
|
||||
</when>
|
||||
<when value="boolfalse">
|
||||
<param name="p1val" value="p1notused" type="text" />
|
||||
</when>
|
||||
</conditional>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="out_file1" format="txt" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="p1use" value="true" />
|
||||
<output name="out_file1">
|
||||
<assert_contents>
|
||||
<has_line line="p1used" />
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
<test>
|
||||
<param name="p1use" value="booltrue" />
|
||||
<output name="out_file1">
|
||||
<assert_contents>
|
||||
<has_line line="p1used" />
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
<test>
|
||||
<param name="p1use" value="false" />
|
||||
<output name="out_file1">
|
||||
<assert_contents>
|
||||
<has_line line="p1notused" />
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
<test>
|
||||
<param name="p1use" value="boolfalse" />
|
||||
<output name="out_file1">
|
||||
<assert_contents>
|
||||
<has_line line="p1notused" />
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
</tests>
|
||||
</tool>
|
||||
@@ -3,6 +3,7 @@
|
||||
<tool file="upload.xml"/>
|
||||
<tool file="simple_constructs.xml" />
|
||||
<tool file="inheritance_simple.xml" />
|
||||
<tool file="boolean_conditional.xml" />
|
||||
<tool file="composite.xml" />
|
||||
<tool file="compare_bam_as_sam.xml" />
|
||||
<tool file="code_file.xml" />
|
||||
|
||||
@@ -61,5 +61,17 @@
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
<test>
|
||||
<!-- Again but using boolean's truevalue -->
|
||||
<param name="p1use" value="true" />
|
||||
<param name="booltest" value="booltrue" />
|
||||
<param name="file" value="simple_line.txt" />
|
||||
<output name="out_file1">
|
||||
<assert_contents>
|
||||
<has_line line="p1used" />
|
||||
<has_line line="booltrue" />
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
</tests>
|
||||
</tool>
|
||||
|
||||
@@ -18,7 +18,7 @@ wormbase_ws225 WormBase WS225 http://ws225.wormbase.org/db/gb2/gbrowse/ caeAng1,
|
||||
tair tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10 arabidopsis_tair8,arabidopsis_tair9,arabidopsis
|
||||
|
||||
#modENCODE
|
||||
modencode modENCODE http://modencode.oicr.on.ca/fgb2/gbrowse/ ce6,dm2 worm,fly
|
||||
modencode modENCODE http://gbrowse.modencode.org/fgb2/gbrowse/ ce10,dm3 worm,fly
|
||||
|
||||
#Saccharomyces Genome Database (SGD)
|
||||
sgd_yeast Saccharomyces Genome Database http://browse.yeastgenome.org/fgb2/gbrowse/ Saccharomyces_cerevisiae_S288C_SGD2010 scgenome
|
||||
|
||||
@@ -1,21 +1,21 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.0">
|
||||
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.1">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top">
|
||||
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/fly" check_values="false" target="_top">
|
||||
<display>go to modENCODE fly server $GALAXY_URL</display>
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm2" >
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm3" >
|
||||
<value_translation>
|
||||
<value galaxy_value="dm2" remote_value="fly" />
|
||||
<value galaxy_value="dm3" remote_value="fly" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="d" missing="" />
|
||||
<value name="dbkey" missing="dm2" />
|
||||
<value name="dbkey" missing="dm3" />
|
||||
<value name="q" missing="" />
|
||||
<value name="s" missing="" />
|
||||
<value name="t" missing="" />
|
||||
|
||||
@@ -1,21 +1,21 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.0">
|
||||
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.1">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top">
|
||||
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/worm" check_values="false" target="_top">
|
||||
<display>go to modENCODE worm server $GALAXY_URL</display>
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce6" >
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce10" >
|
||||
<value_translation>
|
||||
<value galaxy_value="ce6" remote_value="worm" />
|
||||
<value galaxy_value="ce10" remote_value="worm" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="d" missing="" />
|
||||
<value name="dbkey" missing="ce6" />
|
||||
<value name="dbkey" missing="ce10" />
|
||||
<value name="q" missing="" />
|
||||
<value name="s" missing="" />
|
||||
<value name="t" missing="" />
|
||||
|
||||
Reference in New Issue
Block a user