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October 2013

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commit/galaxy-central: greg: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/125a7cafb851/ Changeset: 125a7cafb851 User: greg Date: 2013-10-08 17:56:00 Summary: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular. Affected #: 1 file diff -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd -r 125a7cafb851d9b70195466389acf08dd9b98fd6 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1238,21 +1238,27 @@ log.debug( error_message ) is_valid = False return repository_dependency_tup, is_valid, error_message - # Find the specified changeset revision in the repository's changelog to see if it's valid. - found = False repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - if changeset_hash == changeset_revision: - found = True - break - if not found: - error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ - ( toolshed, name, owner, changeset_revision ) - error_message += "because the changeset revision is invalid. " - log.debug( error_message ) - is_valid = False - return repository_dependency_tup, is_valid, error_message + # The received changeset_revision may be None since defining it in the dependency definition is optional. If this is the case, + # the default will be to set it's value to the repository dependency tip revision. + if changeset_revision is None: + changeset_revision = str( repo.changectx( repo.changelog.tip() ) ) + repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required, str( only_if_compiling_contained_td ) ] + else: + # Find the specified changeset revision in the repository's changelog to see if it's valid. + found = False + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if changeset_hash == changeset_revision: + found = True + break + if not found: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( toolshed, name, owner, changeset_revision ) + error_message += "because the changeset revision is invalid. " + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message else: # Repository dependencies are currently supported within a single tool shed. error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: small fixes for calculating tile height.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/36577eb9f7a4/ Changeset: 36577eb9f7a4 User: jgoecks Date: 2013-10-08 17:45:49 Summary: Trackster: small fixes for calculating tile height. Affected #: 1 file diff -r c0f049223e27a3984dab6b018afa1fce440e6288 -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2128,9 +2128,9 @@ this.low = region.get('start'); this.high = region.get('end'); this.w_scale = w_scale; - // Wrap element in div for background and explicitly set height. Use canvas - // height attribute because canvas may not have height if it is not in document yet. - this.html_elt = $("<div class='track-tile'/>").append(canvas).height( $(canvas).attr("height") ); + this.canvas = canvas; + // Wrap element in div for background and to provide container for tile-specific elements. + this.html_elt = $("<div class='track-tile'/>").append(canvas); this.data = data; this.stale = false; }; @@ -3371,14 +3371,11 @@ // -- Update track, tile heights based on new tile. -- - // Clear any previous height settings for tile. - tile.html_elt.height('auto'); - - // Update max height based on current tile. - this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); + // Update max height based on current tile's canvas. + this.max_height_px = Math.max(this.max_height_px, $(tile.canvas).height()); // Update height for all tiles based on max height. - tile.html_elt.parent().children().css("height", this.max_height_px + "px"); + tile_element.parent().children().css("height", this.max_height_px + "px"); // Update track height based on max height and visible height. var track_height = this.max_height_px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fix for a bug introduced with the rename_to option for the move_file action.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c0f049223e27/ Changeset: c0f049223e27 User: Dave Bouvier Date: 2013-10-08 17:12:10 Summary: Fix for a bug introduced with the rename_to option for the move_file action. Affected #: 1 file diff -r 82b1789621244bd81bf68c28fbe42a29931efee1 -r c0f049223e27a3984dab6b018afa1fce440e6288 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -316,7 +316,8 @@ shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): - source_file = os.path.abspath( os.path.join( current_dir, source ) ) + source_path = os.path.abspath( os.path.join( current_dir, source ) ) + source_file = os.path.basename( source_path ) if rename_to is not None: destination_file = rename_to destination_directory = os.path.join( destination ) @@ -326,7 +327,7 @@ destination_path = os.path.join( destination_directory, source_file ) if not os.path.exists( destination_directory ): os.makedirs( destination_directory ) - shutil.move( source_file, destination_path ) + shutil.move( source_path, destination_path ) def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82b178962124/ Changeset: 82b178962124 User: jgoecks Date: 2013-10-08 16:55:43 Summary: Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view. Affected #: 1 file diff -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 -r 82b1789621244bd81bf68c28fbe42a29931efee1 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -215,7 +215,7 @@ this.name = obj_dict.name; this.view = view; this.container = container; - this.config = new DrawableConfig({ + this.config = new Config({ track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name } @@ -225,7 +225,7 @@ this.track.set_name(this.track.config.values.name); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.drag_handle_class = obj_dict.drag_handle_class; this.is_overview = false; this.action_icons = {}; @@ -285,24 +285,10 @@ title: "Edit settings", css_class: "settings-icon", on_click_fn: function(drawable) { - var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - drawable.config.update_from_form( $(Galaxy.modal.el) ); - Galaxy.modal.hide(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - - // show dialog - Galaxy.modal.show({title: "Configure", body: drawable.config.build_form(), buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); + var view = new ConfigView({ + model: drawable.config + }); + view.render(); } }, // Remove. @@ -911,7 +897,7 @@ this.reset(); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, @@ -1903,22 +1889,30 @@ }; /** - * Container for Drawable configuration data. + * Configuration object. */ -var DrawableConfig = function( options ) { - this.track = options.track; - this.params = options.params; - this.values = {}; - this.restore_values( (options.saved_values ? options.saved_values : {}) ); - this.onchange = options.onchange; -}; - -extend(DrawableConfig.prototype, { +var Config = Backbone.Model.extend({ + initialize: function(options) { + // values is a simple param_key -- value dictionary shared with drawables. + this.set('values', {}); + + // Restore saved values. + if (options.saved_values) { + this.restore_values(options.saved_values); + } + if (options.onchange) { + // HACK: to make onchange work as written, attach track at the + // top level of model and call onchange on custom event. + this.track = options.track; + this.on('change:values', options.onchange, this); + } + }, + /** * Set default value for parameter. */ set_param_default_value: function(key, default_value) { - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1932,7 +1926,7 @@ */ set_param_value: function(key, value) { // Find param. - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1952,8 +1946,10 @@ } // Set value and return true if changed, false otherwise. - if (this.values[key] !== value) { - this.values[key] = value; + if (this.get('values')[key] !== value) { + this.get('values')[key] = value; + // HACK: custom event trigger needed to indicate that values were updated. + this.trigger('change:values'); return true; } else { @@ -1965,21 +1961,25 @@ * Restore config values from a dictionary. */ restore_values: function( values ) { - var track_config = this; - $.each( this.params, function( index, param ) { - if ( values[ param.key ] !== undefined ) { - track_config.values[ param.key ] = values[ param.key ]; - } else { - track_config.values[ param.key ] = param.default_value; - } + var self = this; + _.each( this.get('params'), function(param) { + self.set_param_value(param.key, values[param.key] || param.default_value); }); }, +}); + +var ConfigView = Backbone.View.extend({ + /** - * Build form for modifying parameters. + * Build and show form for modifying configuration. Currently uses Galaxy modals. */ - build_form: function() { - var track_config = this; + render: function() { + // + // Build config selection UI. + // + + var track_config = this.model; var container = $("<div />"); var param; // Function to process parameters recursively @@ -1990,17 +1990,19 @@ if ( param.hidden ) { continue; } // Build row for param var id = 'param_' + index; - var value = track_config.values[ param.key ]; + var value = track_config.get('values')[ param.key ]; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); // Draw parameter as checkbox if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); // Draw parameter as textbox - } else if ( param.type === 'text' ) { + } + else if ( param.type === 'text' ) { row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); // Draw paramter as select area - } else if ( param.type === 'select' ) { + } + else if ( param.type === 'select' ) { var select = $('<select />').attr("id", id); for ( var i = 0; i < param.options.length; i++ ) { $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); @@ -2008,7 +2010,8 @@ select.val( value ); row.append( select ); // Draw parameter as color picker - } else if ( param.type === 'color' ) { + } + else if ( param.type === 'color' ) { var container_div = $("<div/>").appendTo(row), input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") @@ -2071,32 +2074,48 @@ } } // Handle top level parameters in order - handle_params( this.params, container ); - // Return element containing constructed form - return container; + handle_params( track_config.get('params'), container ); + + // + // Use Galaxy modal to display config. + // + + var self = this, + cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + self.update_from_form( $(Galaxy.modal.el) ); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + Galaxy.modal.show({title: "Configure", body: container, buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); }, /** * Update configuration from form. */ update_from_form: function( container ) { - var track_config = this; + var model = this.model; var changed = false; - $.each( this.params, function( index, param ) { - if ( ! param.hidden ) { + _.each(model.get('params'), function(param, index) { + if ( !param.hidden ) { // Get value from form element. var id = 'param_' + index; var value = container.find( '#' + id ).val(); if ( param.type === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } - changed = track_config.set_param_value(param.key, value) || changed; + changed = model.set_param_value(param.key, value) || changed; } }); - if ( changed ) { - this.onchange(); - this.track.changed(); - } } }); @@ -3785,7 +3804,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3793,7 +3812,7 @@ { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: 32, hidden: true } + { key: 'height', type: 'int', default_value: 30, hidden: true } ], saved_values: obj_dict.prefs, onchange: function() { @@ -3802,8 +3821,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { @@ -3844,7 +3863,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3862,8 +3881,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** @@ -3899,7 +3918,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3922,8 +3941,8 @@ track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; this.container_div.addClass( "feature-track" ); this.show_labels_scale = 0.001; @@ -4207,7 +4226,7 @@ this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; TiledTrack.call(this, view, container, obj_dict); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4223,7 +4242,7 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.painter = painters.VariantPainter; this.summary_draw_height = 30; @@ -4363,7 +4382,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4383,8 +4402,8 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - + this.prefs = this.config.get('values'); + // Choose painter based on whether there is reference data. this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: better reconciling of hda states within history and hda collection
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/402c90f647b6/ Changeset: 402c90f647b6 User: carlfeberhard Date: 2013-10-08 16:47:43 Summary: History panel: better reconciling of hda states within history and hda collection Affected #: 3 files diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -48,7 +48,7 @@ /** HDACollection of the HDAs contained in this history. */ this.hdas = new HDACollection(); - + /** the setTimeout id for any updater currently set */ this.updateTimeoutId = null; // if we've got hdas passed in the constructor, load them and set up updates if needed @@ -57,10 +57,14 @@ this.checkForUpdates(); //TODO: don't call if force_history_refresh if( this.hdas.length > 0 ){ - this.updateDisplayApplications(); + this.fetchDisplayApplications(); } } + this.setHdaEventHandlers(); + this.setOwnEventHandlers(); + }, + setHdaEventHandlers : function(){ // if an hda moves into the ready state and has the force_history_refresh flag (often via tool.xml) // then: refresh the panel this.hdas.bind( 'state:ready', function( hda, newState, oldState ){ @@ -68,7 +72,9 @@ this.updateAfterDelay(); } }, this ); + }, + setOwnEventHandlers : function(){ if( this.logger ){ this.bind( 'all', function( event ){ this.log( this + '', arguments ); @@ -88,84 +94,86 @@ updateAfterDelay : function(){ var history = this; this.updateTimeoutId = setTimeout( function(){ + history.updateTimeoutId = null; history.stateUpdater(); }, History.UPDATE_DELAY ); return this.updateTimeoutId; }, - // get the history's state from it's cummulative ds states, delay + update if needed - // events: ready + isRunning : function(){ + var historyState = this.get( 'state' ); + // set up to keep pulling if this history in run/queue state + //note: the state strings btwn history & hda are shared on the server (or a subset of) + return ( ( historyState === HistoryDatasetAssociation.STATES.RUNNING ) + ||( historyState === HistoryDatasetAssociation.STATES.QUEUED ) ); + }, + + isReady : function(){ + return !this.isRunning(); + }, + checkForUpdates : function(){ - // get overall History state from collection, run updater if History has running/queued hdas - // boiling it down on the client to running/not - if( this.hdas.running().length ){ + // set up to keep pulling if this history in run/queue state + if( this.isRunning() ){ this.updateAfterDelay(); + // otherwise, we're now in a 'ready' state (no hdas running) } else { this.trigger( 'ready' ); } return this; }, - // update this history, find any hda's running/queued, update ONLY those that have changed states, - // set up to run this again in some interval of time + findHdasToUpdate : function(){ + var history = this, + state_ids = history.get( 'state_ids' ), + changedIds = []; + + // get a list of hda ids for hdas we need to get more info on + _.each( state_ids, function( list, stateAccrdToHistory ){ + _.each( list, function( id ){ + var hda = history.hdas.get( id ); + // if the id is not in the current hda list + // or the state doesn't match the state rpt. by the history - save that id + if( !hda || hda.get( 'state' ) !== stateAccrdToHistory ){ + changedIds.push( id ); + } + }); + }); + return changedIds; + }, + + // fetch new data for this history, + // compare the state_ids from that with the current list and fetch updates for new or changed hdas + // if the history still has non-ready hdas, set up to run this again in some interval of time // events: ready stateUpdater : function(){ //TODO: we need to get states from one location: history_contents (right now it's both history and contents) var history = this, oldState = this.get( 'state' ), - // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state - oldStateIds = this.get( 'state_ids' ); + historyXhr = this.fetch(); // pull from the history api - //TODO: fetch? - jQuery.ajax( 'api/histories/' + this.get( 'id' ) - - ).success( function( response ){ + historyXhr.done( function( newHistoryModel ){ //this.log( 'historyApiRequest, response:', response ); - history.set( response ); - history.log( 'current history state:', history.get( 'state' ), - '(was)', oldState, + history.set( newHistoryModel ); + history.log( 'current history state:', history.get( 'state' ), '(was)', oldState, 'new size:', history.get( 'nice_size' ) ); - //TODO: revisit this - seems too elaborate, need something straightforward - // for each state, check for the difference between old dataset states and new - // the goal here is to check ONLY those datasets that have changed states (not all datasets) - var changedIds = []; - _.each( _.keys( response.state_ids ), function( state ){ - var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); - // aggregate those changed ids - changedIds = changedIds.concat( diffIds ); - }); - // send the changed ids (if any) to dataset collection to have them fetch their own model changes - if( changedIds.length ){ - history.fetchHdaUpdates( changedIds ) - .done( function(){ - furtherUpdatesOrReady( history ); + var hdaIdsToUpdate = history.findHdasToUpdate(); + if( hdaIdsToUpdate.length ){ + // simplify with empty promise when no ids + history.fetchHdaUpdates( hdaIdsToUpdate ) + .done( function( models ){ + history.checkForUpdates(); }); } else { - furtherUpdatesOrReady( history ); + history.checkForUpdates(); } - function furtherUpdatesOrReady( history ){ - var timeout; - // set up to keep pulling if this history in run/queue state - if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.SETTING_METADATA )){ - //|| ( history.hdas.running() ) ){ - timeout = history.updateAfterDelay(); - - // otherwise, we're now in a 'ready' state (no hdas running) - } else { - this.updateTimeoutId = null; - history.trigger( 'ready' ); - } - return timeout; - } - - }).error( function( xhr, status, error ){ + }); + historyXhr.fail( function( xhr, status, error ){ //TODO: use ajax.status handlers here // keep rolling on a bad gateway - server restart if( xhr.status === 502 ){ @@ -197,9 +205,7 @@ xhr = jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), - /** - * @inner - */ + /** @inner */ error : function( xhr, status, error ){ if( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ){ return; } @@ -286,11 +292,10 @@ * @param {String[]} ids an array of hda ids to update (optional, defaults to all hdas) * @returns {HistoryDatasetAssociation[]} hda models that were updated */ - updateDisplayApplications : function( ids ){ - this.log( this + 'updateDisplayApplications:', ids ); + fetchDisplayApplications : function( ids ){ + this.log( this + '.fetchDisplayApplications:', ids ); var history = this, - // data = { id: this.get( 'id' ) }; - //if( ids && _.isArray( ids ) ){ data.hda_ids = ids.join( ',' ); } + // if any ids passed place them in the query string data data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); //TODO: hardcoded diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)||(h.get("state")===HistoryDatasetAssociation.STATES.SETTING_METADATA)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -198,8 +198,11 @@ // 2. from console: new PersistentStorage( '__history_panel' ).set( 'debugging', true ) // -> history panel and hdas will display console logs in console var debugging = false; - if( jQuery.jStorage.get( '__history_panel' ) ){ + if( sessionStorage.getItem( '__history_panel' ) ){ debugging = new PersistentStorage( '__history_panel' ).get( 'debugging' ); + if( debugging ){ + console.debug( '(debugging)' ); + } } // get the current user (either from the top frame's Galaxy or if in tab via the bootstrap) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 11 new changesets
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26e7555cd499/ Changeset: 26e7555cd499 User: fubar Date: 2013-10-08 01:24:59 Summary: hg backout -r 1092b0d backout unintended commits to tophat and bowtie2 wrappers Affected #: 3 files diff -r f76c280cdee539b65315ac583f93bfa52feb790d -r 26e7555cd49967ab01f003abc6168f885bbe0dd1 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -126,14 +126,6 @@ </command><inputs> - <param name="jobname" type="text" value="Tophat2" size="80" label="Job title for outputs" - help="Output name to remind you what this was for"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - </param><conditional name="singlePaired"><param name="sPaired" type="select" label="Is this library mate-paired?"><option value="single">Single-end</option> @@ -281,19 +273,19 @@ </stdio><outputs> - <data format="tabular" name="fusions" label="${on_string}_${jobname}_fusions.xls" from_work_dir="tophat_out/fusions.out"> + <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"><filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data> - <data format="bed" name="insertions" label="${on_string}_${jobname}_ins.bed" from_work_dir="tophat_out/insertions.bed"> + <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="deletions" label="${on_string}_${jobname}_del.bed" from_work_dir="tophat_out/deletions.bed"> + <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="junctions" label="${on_string}_${jobname}_splicejunc.bed" from_work_dir="tophat_out/junctions.bed"> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"><expand macro="dbKeyActions" /></data> - <data format="bam" name="accepted_hits" label="${on_string}_${jobname}_hits.bam" from_work_dir="tophat_out/accepted_hits.bam"> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"><expand macro="dbKeyActions" /></data></outputs> diff -r f76c280cdee539b65315ac583f93bfa52feb790d -r 26e7555cd49967ab01f003abc6168f885bbe0dd1 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -27,7 +27,6 @@ from rgutils import getFileString import zipfile import gzip -import bz2 class FastQC(): """wrapper @@ -63,43 +62,27 @@ infname = self.opts.inputfilename linf = infname.lower() trimext = False - isgz = False - isbz2 = False - iszip = False # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf # patched may 29 2013 until this is fixed properly - f = gzip.open(self.opts.input) - try: + if ( linf.endswith('.gz') or linf.endswith('.gzip') ): + f = gzip.open(self.opts.input) + try: testrow = f.readline() - if not (linf.endswith('.gz') or linf.endswith('.gzip')): - isgz = True - except: - if linf.endswith('.gz') or linf.endswith('.gzip'): - trimext = True - f.close() - f = bz2.BZ2File(self.opts.input) - try: - x = read(f,2) # will work if a real bz2 - if not linf.endswith('bz2'): - isbz2 = True - except: - if linf.endswith('bz2'): - trimext = True - f.close() - if zipfile.is_zipfile(self.opts.input): - if not linf.endswith('.zip'): - iszip = True - else: - if linf.endswith('.zip'): - trimext = True + except: + trimext = True + f.close() + elif linf.endswith('bz2'): + f = bz2.open(self.opts.input,'rb') + try: + f.readline() + except: + trimext = True + f.close() + elif linf.endswith('.zip'): + if not zipfile.is_zipfile(self.opts.input): + trimext = True if trimext: infname = os.path.splitext(infname)[0] - elif isgz: - infname = '%s.gz' % infname - elif isbz2: - infname = '%s.bzip2' % infname - elif iszip: - infname = '%s.zip' % infname fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) diff -r f76c280cdee539b65315ac583f93bfa52feb790d -r 26e7555cd49967ab01f003abc6168f885bbe0dd1 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -87,22 +87,23 @@ ## read group information #if str($read_group.selection) == "yes": #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm: - --rg-id "$read_group.rgid" - --rg "LB:$read_group.rglb" - --rg "PL:$read_group.rgpl" - --rg "SM:$read_group.rgsm" + --rg-id $read_group.rgid + --rg LB:$read_group.rglb + --rg PL:$read_group.rgpl + --rg SM:$read_group.rgsm #end if #end if ## view/sort and output file - | samtools view -Su - | samtools sort -o - - > $output + | samtools view -Su - | samtools sort -o - - > $output; ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - ;mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r + + mv $left $output_unaligned_reads_l; + mv $right $output_unaligned_reads_r; #end if </command> @@ -112,8 +113,6 @@ </stdio><inputs> - <param name="jobtitle" type="text" value="bowtie2" label="Memorable short reminder of this job's importance for outputs" /> - <conditional name="library"><param name="type" type="select" label="Is this library mate-paired?"> @@ -217,7 +216,7 @@ <outputs> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_${jobtitle}_unaligL.fastq" > + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" ><filter>unaligned_file is True</filter><actions><action type="format"> @@ -225,7 +224,7 @@ </action></actions></data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_${jobtitle}_unaligR.fastq)"> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"><filter>library['type'] == "paired" and unaligned_file is True</filter><actions><action type="format"> @@ -233,7 +232,7 @@ </action></actions></data> - <data format="bam" name="output" label="${on_string}_${jobtitle}_aligned.bam"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="reference_genome.source"><when value="indexed"> @@ -255,17 +254,6 @@ </outputs><tests> - <test> -  - <param name="type" value="single"/> - <param name="selection" value="no"/> - <param name="full" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/> - <param name="own_file" value="bowtie2/phix_genome.fasta" /> - <output name="output" file="bowtie2/phix_mapped.bam" /> - </test></tests><help> https://bitbucket.org/galaxy/galaxy-central/commits/962d981799cf/ Changeset: 962d981799cf User: fubar Date: 2013-10-08 01:50:10 Summary: backout -r 10799 Affected #: 191 files diff -r 26e7555cd49967ab01f003abc6168f885bbe0dd1 -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 tools/rgedgeR/rgToolFactory.py --- a/tools/rgedgeR/rgToolFactory.py +++ /dev/null @@ -1,605 +0,0 @@ -# rgToolFactory.py -# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 -# -# all rights reserved -# Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# july 2013 -# added ability to combine images and individual log files into html output -# just make sure there's a log file foo.log and it will be output -# together with all images named like "foo_*.pdf -# otherwise old format for html -# -# January 2013 -# problem pointed out by Carlos Borroto -# added escaping for <>$ - thought I did that ages ago... -# -# August 11 2012 -# changed to use shell=False and cl as a sequence - -# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. -# It also serves as the wrapper for the new tool. -# -# you paste and run your script -# Only works for simple scripts that read one input from the history. -# Optionally can write one new history dataset, -# and optionally collect any number of outputs into links on an autogenerated HTML page. - -# DO NOT install on a public or important site - please. - -# installed generated tools are fine if the script is safe. -# They just run normally and their user cannot do anything unusually insecure -# but please, practice safe toolshed. -# Read the fucking code before you install any tool -# especially this one - -# After you get the script working on some test data, you can -# optionally generate a toolshed compatible gzip file -# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for -# safe and largely automated installation in a production Galaxy. - -# If you opt for an HTML output, you get all the script outputs arranged -# as a single Html history item - all output files are linked, thumbnails for all the pdfs. -# Ugly but really inexpensive. -# -# Patches appreciated please. -# -# -# long route to June 2012 product -# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them -# derived from an integrated script model -# called rgBaseScriptWrapper.py -# Note to the unwary: -# This tool allows arbitrary scripting on your Galaxy as the Galaxy user -# There is nothing stopping a malicious user doing whatever they choose -# Extremely dangerous!! -# Totally insecure. So, trusted users only -# -# preferred model is a developer using their throw away workstation instance - ie a private site. -# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. -# - -import sys -import shutil -import subprocess -import os -import time -import tempfile -import optparse -import tarfile -import re -import shutil -import math - -progname = os.path.split(sys.argv[0])[1] -myversion = 'V000.2 June 2012' -verbose = False -debug = False -toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -html_escape_table = { - "&": "&", - ">": ">", - "<": "<", - "$": "\$" - } - -def html_escape(text): - """Produce entities within text.""" - return "".join(html_escape_table.get(c,c) for c in text) - -def cmd_exists(cmd): - return subprocess.call("type " + cmd, shell=True, - stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 - - -class ScriptRunner: - """class is a wrapper for an arbitrary script - """ - - def __init__(self,opts=None,treatbashSpecial=True): - """ - cleanup inputs, setup some outputs - - """ - self.useGM = cmd_exists('gm') - self.useIM = cmd_exists('convert') - self.useGS = cmd_exists('gs') - self.treatbashSpecial = treatbashSpecial - if opts.output_dir: # simplify for the tool tarball - os.chdir(opts.output_dir) - self.thumbformat = 'png' - self.opts = opts - self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. - self.toolid = self.toolname - self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later - self.pyfile = self.myname # crude but efficient - the cruft won't hurt much - self.xmlfile = '%s.xml' % self.toolname - s = open(self.opts.script_path,'r').readlines() - s = [x.rstrip() for x in s] # remove pesky dos line endings if needed - self.script = '\n'.join(s) - fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) - tscript = open(self.sfile,'w') # use self.sfile as script source for Popen - tscript.write(self.script) - tscript.close() - self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help - self.escapedScript = '\n'.join([html_escape(x) for x in s]) - self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname) - if opts.output_dir: # may not want these complexities - self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) - art = '%s.%s' % (self.toolname,opts.interpreter) - artpath = os.path.join(self.opts.output_dir,art) # need full path - artifact = open(artpath,'w') # use self.sfile as script source for Popen - artifact.write(self.script) - artifact.close() - self.cl = [] - self.html = [] - a = self.cl.append - a(opts.interpreter) - if self.treatbashSpecial and opts.interpreter in ['bash','sh']: - a(self.sfile) - else: - a('-') # stdin - a(opts.input_tab) - a(opts.output_tab) - self.outFormats = 'tabular' # TODO make this an option at tool generation time - self.inputFormats = 'tabular' # TODO make this an option at tool generation time - self.test1Input = '%s_test1_input.xls' % self.toolname - self.test1Output = '%s_test1_output.xls' % self.toolname - self.test1HTML = '%s_test1_output.html' % self.toolname - - def makeXML(self): - """ - Create a Galaxy xml tool wrapper for the new script as a string to write out - fixme - use templating or something less fugly than this example of what we produce - - <tool id="reverse" name="reverse" version="0.01"> - <description>a tabular file</description> - <command interpreter="python"> - reverse.py --script_path "$runMe" --interpreter "python" - --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" - </command> - <inputs> - <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> - - </inputs> - <outputs> - <data format="tabular" name="tab_file" label="${job_name}"/> - - </outputs> - <help> - -**What it Does** - -Reverse the columns in a tabular file - - </help> - <configfiles> - <configfile name="runMe"> - -# reverse order of columns in a tabular file -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r') -o = open(outp,'w') -for row in i: - rs = row.rstrip().split('\t') - rs.reverse() - o.write('\t'.join(rs)) - o.write('\n') -i.close() -o.close() - - - </configfile> - </configfiles> - </tool> - - """ - newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> - %(tooldesc)s - %(command)s - <inputs> - %(inputs)s - </inputs> - <outputs> - %(outputs)s - </outputs> - <configfiles> - <configfile name="runMe"> - %(script)s - </configfile> - </configfiles> - %(tooltests)s - <help> - %(help)s - </help> - </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto - - newCommand="""<command interpreter="python"> - %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" - --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s - </command>""" # may NOT be an input or htmlout - tooltestsTabOnly = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="tab_file" file="%(test1Output)s" ftype="tabular"/> - </test></tests>""" - tooltestsHTMLOnly = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> - </test></tests>""" - tooltestsBoth = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="tab_file" file="%(test1Output)s" ftype="tabular" /> - <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> - </test></tests>""" - xdict = {} - xdict['tool_version'] = self.opts.tool_version - xdict['test1Input'] = self.test1Input - xdict['test1HTML'] = self.test1HTML - xdict['test1Output'] = self.test1Output - if self.opts.make_HTML and self.opts.output_tab <> 'None': - xdict['tooltests'] = tooltestsBoth % xdict - elif self.opts.make_HTML: - xdict['tooltests'] = tooltestsHTMLOnly % xdict - else: - xdict['tooltests'] = tooltestsTabOnly % xdict - xdict['script'] = self.escapedScript - # configfile is least painful way to embed script to avoid external dependencies - # but requires escaping of <, > and $ to avoid Mako parsing - if self.opts.help_text: - xdict['help'] = open(self.opts.help_text,'r').read() - else: - xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' - coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] - coda.append(self.indentedScript) - coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow())) - coda.append('See %s for details of that project' % (toolFactoryURL)) - coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ') - coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573') - xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) - if self.opts.tool_desc: - xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc - else: - xdict['tooldesc'] = '' - xdict['command_outputs'] = '' - xdict['outputs'] = '' - if self.opts.input_tab <> 'None': - xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something - xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats - else: - xdict['command_inputs'] = '' # assume no input - eg a random data generator - xdict['inputs'] = '' - xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname - xdict['toolname'] = self.toolname - xdict['toolid'] = self.toolid - xdict['interpreter'] = self.opts.interpreter - xdict['scriptname'] = self.sfile - if self.opts.make_HTML: - xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" ' - xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' - if self.opts.output_tab <> 'None': - xdict['command_outputs'] += ' --output_tab "$tab_file"' - xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats - xdict['command'] = newCommand % xdict - xmls = newXML % xdict - xf = open(self.xmlfile,'w') - xf.write(xmls) - xf.write('\n') - xf.close() - # ready for the tarball - - - def makeTooltar(self): - """ - a tool is a gz tarball with eg - /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... - """ - retval = self.run() - if retval: - print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' - sys.exit(1) - self.makeXML() - tdir = self.toolname - os.mkdir(tdir) - if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. - testdir = os.path.join(tdir,'test-data') - os.mkdir(testdir) # make tests directory - shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) - if self.opts.output_tab <> 'None': - shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) - if self.opts.make_HTML: - shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) - if self.opts.output_dir: - shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) - op = '%s.py' % self.toolname # new name - outpiname = os.path.join(tdir,op) # path for the tool tarball - pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) - notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),] - notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) - notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) - pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm - notes += pi - outpi = open(outpiname,'w') - outpi.write(''.join(notes)) - outpi.write('\n') - outpi.close() - stname = os.path.join(tdir,self.sfile) - if not os.path.exists(stname): - shutil.copyfile(self.sfile, stname) - xtname = os.path.join(tdir,self.xmlfile) - if not os.path.exists(xtname): - shutil.copyfile(self.xmlfile,xtname) - tarpath = "%s.gz" % self.toolname - tar = tarfile.open(tarpath, "w:gz") - tar.add(tdir,arcname=self.toolname) - tar.close() - shutil.copyfile(tarpath,self.opts.new_tool) - shutil.rmtree(tdir) - ## TODO: replace with optional direct upload to local toolshed? - return retval - - - def compressPDF(self,inpdf=None,thumbformat='png'): - """need absolute path to pdf - """ - assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) - hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname) - sto = open(hlog,'w') - outpdf = '%s_compressed' % inpdf - cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] - x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - retval1 = x.wait() - if retval1 == 0: - os.unlink(inpdf) - shutil.move(outpdf,inpdf) - outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) - if self.useGM: - cl2 = ['gm convert', inpdf, outpng] - else: # assume imagemagick - cl2 = ['convert', inpdf, outpng] - x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - retval2 = x.wait() - sto.close() - retval = retval1 or retval2 - return retval - - - def getfSize(self,fpath,outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath,fpath) - if os.path.isfile(fp): - size = '0 B' - n = float(os.path.getsize(fp)) - if n > 2**20: - size = '%1.1f MB' % (n/2**20) - elif n > 2**10: - size = '%1.1f KB' % (n/2**10) - elif n > 0: - size = '%d B' % (int(n)) - return size - - def makeHtml(self): - """ Create an HTML file content to list all the artifacts found in the output_dir - """ - - galhtmlprefix = """<!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><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> - <title></title> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="toolFormBody"> - """ - galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" - galhtmlpostfix = """</div></body></html>\n""" - - flist = os.listdir(self.opts.output_dir) - flist = [x for x in flist if x <> 'Rplots.pdf'] - flist.sort() - html = [] - html.append(galhtmlprefix % progname) - html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections - logfiles.sort() - logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)] - logfiles.append(os.path.abspath(self.tlog)) # make it the last one - pdflist = [] - npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) - for rownum,fname in enumerate(flist): - dname,e = os.path.splitext(fname) - sfsize = self.getfSize(fname,self.opts.output_dir) - if e.lower() == '.pdf' : # compress and make a thumbnail - thumb = '%s.%s' % (dname,self.thumbformat) - pdff = os.path.join(self.opts.output_dir,fname) - retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) - if retval == 0: - pdflist.append((fname,thumb)) - if (rownum+1) % 2 == 0: - fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - else: - fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - for logfname in logfiles: # expect at least tlog - if more - if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later - sectionname = 'All tool run' - if (len(logfiles) > 1): - sectionname = 'Other' - ourpdfs = pdflist - else: - realname = os.path.basename(logfname) - sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log - ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] - pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove - nacross = 1 - npdf = len(ourpdfs) - - if npdf > 0: - nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) - if int(nacross)**2 != npdf: - nacross += 1 - nacross = int(nacross) - width = min(400,int(1200/nacross)) - html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) - html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') - ntogo = nacross # counter for table row padding with empty cells - html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') - for i,paths in enumerate(ourpdfs): - fname,thumb = paths - s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" - alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) - if ((i+1) % nacross == 0): - s += '</tr>\n' - ntogo = 0 - if i < (npdf - 1): # more to come - s += '<tr>' - ntogo = nacross - else: - ntogo -= 1 - html.append(s) - if html[-1].strip().endswith('</tr>'): - html.append('</table></div>\n') - else: - if ntogo > 0: # pad - html.append('<td> </td>'*ntogo) - html.append('</tr></table></div>\n') - logt = open(logfname,'r').readlines() - logtext = [x for x in logt if x.strip() > ''] - html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) - if len(logtext) > 1: - html.append('\n<pre>\n') - html += logtext - html.append('\n</pre>\n') - else: - html.append('%s is empty<br/>' % logfname) - if len(fhtml) > 0: - fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') - fhtml.append('</table></div><br/>') - html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) - html.append(galhtmlpostfix) - htmlf = file(self.opts.output_html,'w') - htmlf.write('\n'.join(html)) - htmlf.write('\n') - htmlf.close() - self.html = html - - - def run(self): - """ - scripts must be small enough not to fill the pipe! - """ - if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: - retval = self.runBash() - else: - if self.opts.output_dir: - ste = open(self.elog,'w') - sto = open(self.tlog,'w') - sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) - p.stdin.write(self.script) - p.stdin.close() - retval = p.wait() - if self.opts.output_dir: - sto.close() - ste.close() - err = open(self.elog,'r').readlines() - if retval <> 0 and err: # problem - print >> sys.stderr,err - if self.opts.make_HTML: - self.makeHtml() - return retval - - def runBash(self): - """ - cannot use - for bash so use self.sfile - """ - if self.opts.output_dir: - s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) - sto = open(self.tlog,'w') - sto.write(s) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False) - retval = p.wait() - if self.opts.output_dir: - sto.close() - if self.opts.make_HTML: - self.makeHtml() - return retval - - -def main(): - u = """ - This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: - <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" - </command> - """ - op = optparse.OptionParser() - a = op.add_option - a('--script_path',default=None) - a('--tool_name',default=None) - a('--interpreter',default=None) - a('--output_dir',default=None) - a('--output_html',default=None) - a('--input_tab',default="None") - a('--output_tab',default="None") - a('--user_email',default='Unknown') - a('--bad_user',default=None) - a('--make_Tool',default=None) - a('--make_HTML',default=None) - a('--help_text',default=None) - a('--tool_desc',default=None) - a('--new_tool',default=None) - a('--tool_version',default=None) - opts, args = op.parse_args() - assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user) - assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' - assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' - assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' - if opts.output_dir: - try: - os.makedirs(opts.output_dir) - except: - pass - r = ScriptRunner(opts) - if opts.make_Tool: - retcode = r.makeTooltar() - else: - retcode = r.run() - os.unlink(r.sfile) - if retcode: - sys.exit(retcode) # indicate failure to job runner - - -if __name__ == "__main__": - main() - - diff -r 26e7555cd49967ab01f003abc6168f885bbe0dd1 -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 tools/rgedgeR/rgedgeRpaired.xml --- a/tools/rgedgeR/rgedgeRpaired.xml +++ /dev/null @@ -1,1080 +0,0 @@ -<tool id="rgDifferentialCount" name="Differential_Count" version="0.20"> - <description>models using BioConductor packages</description> - <requirements> - <requirement type="package" version="2.12">biocbasics</requirement> - <requirement type="package" version="3.0.1">r3</requirement> - <requirement type="package" version="1.3.18">graphicsmagick</requirement> - <requirement type="package" version="9.07">ghostscript</requirement> - </requirements> - - <command interpreter="python"> - rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" - --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" - </command> - <inputs> - <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample" - help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/> - <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" - help="Supply a meaningful name here to remind you what the outputs contain"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/> - <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" - multiple="true" use_header_names="true" size="120" display="checkboxes"> - <validator type="no_options" message="Please select at least one column."/> - </param> - <param name="control_name" type="text" value="Control" size="50" label="Control Name"/> - <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" - multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true"> - </param> - <param name="subjectids" type="text" optional="true" size="120" value = "" - label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input" - help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="," /></valid> - </sanitizer> - </param> - <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs" - help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/> - <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" - label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples" - help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/> - - <conditional name="edgeR"> - <param name="doedgeR" type="select" - label="Run this model using edgeR" - help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates"> - <option value="F">Do not run edgeR</option> - <option value="T" selected="true">Run edgeR</option> - </param> - <when value="T"> - <param name="edgeR_priordf" type="integer" value="20" size="3" - label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n and prior.df = prior.n * residual.df" - help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/> - </when> - <when value="F"></when> - </conditional> - <conditional name="DESeq2"> - <param name="doDESeq2" type="select" - label="Run the same model with DESeq2 and compare findings" - help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR"> - <option value="F" selected="true">Do not run DESeq2</option> - <option value="T">Run DESeq2</option> - </param> - <when value="T"> - <param name="DESeq_fitType" type="select"> - <option value="parametric" selected="true">Parametric (default) fit for dispersions</option> - <option value="local">Local fit - this will automagically be used if parametric fit fails</option> - <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option> - </param> - </when> - <when value="F"></when> - </conditional> - <param name="doVoom" type="select" - label="Run the same model with Voom/limma and compare findings" - help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma"> - <option value="F" selected="true">Do not run VOOM</option> - <option value="T">Run VOOM</option> - </param> - <conditional name="camera"> - <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" - help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history"> - <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option> - <option value="T">Run GSEA tests with the Camera algorithm</option> - </param> - <when value="T"> - <conditional name="gmtSource"> - <param name="refgmtSource" type="select" - label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set"> - <option value="indexed" selected="true">Use a built-in gene set</option> - <option value="history">Use a gene set from my history</option> - <option value="both">Add a gene set from my history to a built in gene set</option> - </param> - <when value="indexed"> - <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> - <options from_data_table="gseaGMT_3.1"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No GMT v3.1 files are available - please install them"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" /> - </when> - <when value="both"> - <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" /> - <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> - <options from_data_table="gseaGMT_4"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/> - </options> - </param> - </when> - </conditional> - </when> - <when value="F"> - </when> - </conditional> - <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control" - help="Conventional default value of 0.05 recommended"/> - <param name="fdrtype" type="select" label="FDR (Type II error) control method" - help="Use fdr or bh typically to control for the number of tests in a reliable way"> - <option value="fdr" selected="true">fdr</option> - <option value="BH">Benjamini Hochberg</option> - <option value="BY">Benjamini Yukateli</option> - <option value="bonferroni">Bonferroni</option> - <option value="hochberg">Hochberg</option> - <option value="holm">Holm</option> - <option value="hommel">Hommel</option> - <option value="none">no control for multiple tests</option> - </param> - </inputs> - <outputs> - <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls"> - <filter>edgeR['doedgeR'] == "T"</filter> - </data> - <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls"> - <filter>DESeq2['doDESeq2'] == "T"</filter> - </data> - <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls"> - <filter>doVoom == "T"</filter> - </data> - <data format="html" name="html_file" label="${title}.html"/> - </outputs> - <stdio> - <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" /> - </stdio> - <tests> -<test> -<param name='input1' value='test_bams2mx.xls' ftype='tabular' /> - <param name='treatment_name' value='case' /> - <param name='title' value='edgeRtest' /> - <param name='useNDF' value='' /> - <param name='doedgeR' value='T' /> - <param name='doVoom' value='T' /> - <param name='doDESeq2' value='T' /> - <param name='fdrtype' value='fdr' /> - <param name='edgeR_priordf' value="8" /> - <param name='fdrthresh' value="0.05" /> - <param name='control_name' value='control' /> - <param name='subjectids' value='' /> - <param name='Treat_cols' value='3,4,5,9' /> - <param name='Control_cols' value='2,6,7,8' /> - <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' /> - <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' /> -</test> -</tests> - -<configfiles> -<configfile name="runme"> -<![CDATA[ -# -# edgeR.Rscript -# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross -# Performs DGE on a count table containing n replicates of two conditions -# -# Parameters -# -# 1 - Output Dir - -# Original edgeR code by: S.Lunke and A.Kaspi -reallybig = log10(.Machine\$double.xmax) -reallysmall = log10(.Machine\$double.xmin) -library('stringr') -library('gplots') -library('edgeR') -hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here') -{ -# Perform clustering for significant pvalues after controlling FWER - samples = colnames(cmat) - gu = unique(group) - gn = rownames(cmat) - if (length(gu) == 2) { - col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"} - pcols = unlist(lapply(group,col.map)) - } else { - colours = rainbow(length(gu),start=0,end=4/6) - pcols = colours[match(group,gu)] } - dm = cmat[(! is.na(gn)),] - # remove unlabelled hm rows - nprobes = nrow(dm) - # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance') - if (nprobes > nsamp) { - dm =dm[1:nsamp,] - #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total') - } - newcolnames = substr(colnames(dm),1,20) - colnames(dm) = newcolnames - pdf(outpdfname) - heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none', - Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5) - dev.off() -} - -hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here") -{ - # for 2 groups only was - #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"} - #pcols = unlist(lapply(group,col.map)) - gu = unique(group) - colours = rainbow(length(gu),start=0.3,end=0.6) - pcols = colours[match(group,gu)] - nrows = nrow(cmat) - mtitle = paste(myTitle,'Heatmap: n contigs =',nrows) - if (nrows > nsamp) { - cmat = cmat[c(1:nsamp),] - mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='') - } - newcolnames = substr(colnames(cmat),1,20) - colnames(cmat) = newcolnames - pdf(outpdfname) - heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols) - dev.off() -} - -qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...) -# stolen from https://gist.github.com/703512 -{ - o = -log10(sort(pvector,decreasing=F)) - e = -log10( 1:length(o)/length(o) ) - o[o==-Inf] = reallysmall - o[o==Inf] = reallybig - maint = descr - pdf(outpdf) - plot(e,o,pch=19,cex=1, main=maint, ..., - xlab=expression(Expected~~-log[10](italic(p))), - ylab=expression(Observed~~-log[10](italic(p))), - xlim=c(0,max(e)), ylim=c(0,max(o))) - lines(e,e,col="red") - grid(col = "lightgray", lty = "dotted") - dev.off() -} - -smearPlot = function(DGEList,deTags, outSmear, outMain) - { - pdf(outSmear) - plotSmear(DGEList,de.tags=deTags,main=outMain) - grid(col="lightgray", lty="dotted") - dev.off() - } - -boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname) -{ # - nc = ncol(rawrs) - for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA} - fullnames = colnames(rawrs) - newcolnames = substr(colnames(rawrs),1,20) - colnames(rawrs) = newcolnames - newcolnames = substr(colnames(cleanrs),1,20) - colnames(cleanrs) = newcolnames - defpar = par(no.readonly=T) - print.noquote('raw contig counts by sample:') - print.noquote(summary(rawrs)) - print.noquote('normalised contig counts by sample:') - print.noquote(summary(cleanrs)) - pdf(pdfname) - par(mfrow=c(1,2)) - boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint)) - grid(col="lightgray",lty="dotted") - boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint)) - grid(col="lightgray",lty="dotted") - dev.off() - pdfname = "sample_counts_histogram.pdf" - nc = ncol(rawrs) - print.noquote(paste('Using ncol rawrs=',nc)) - ncroot = round(sqrt(nc)) - if (ncroot*ncroot < nc) { ncroot = ncroot + 1 } - m = c() - for (i in c(1:nc)) { - rhist = hist(rawrs[,i],breaks=100,plot=F) - m = append(m,max(rhist\$counts)) - } - ymax = max(m) - ncols = length(fullnames) - if (ncols > 20) - { - scale = 7*ncols/20 - pdf(pdfname,width=scale,height=scale) - } else { - pdf(pdfname) - } - par(mfrow=c(ncroot,ncroot)) - for (i in c(1:nc)) { - hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", - breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax)) - } - dev.off() - par(defpar) - -} - -cumPlot = function(rawrs,cleanrs,maint,myTitle) -{ # updated to use ecdf - pdfname = "Filtering_rowsum_bar_charts.pdf" - defpar = par(no.readonly=T) - lrs = log(rawrs,10) - lim = max(lrs) - pdf(pdfname) - par(mfrow=c(2,1)) - hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)", - ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1) - grid(col="lightgray", lty="dotted") - lrs = log(cleanrs,10) - hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)", - ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1) - grid(col="lightgray", lty="dotted") - dev.off() - par(defpar) -} - -cumPlot1 = function(rawrs,cleanrs,maint,myTitle) -{ # updated to use ecdf - pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_') - pdf(pdfname) - par(mfrow=c(2,1)) - lastx = max(rawrs) - rawe = knots(ecdf(rawrs)) - cleane = knots(ecdf(cleanrs)) - cy = 1:length(cleane)/length(cleane) - ry = 1:length(rawe)/length(rawe) - plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads", - ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle) - grid(col="blue") - plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads", - ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle) - grid(col="blue") - dev.off() -} - - - -doGSEAold = function(y=NULL,design=NULL,histgmt="", - bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", - ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH") -{ - sink('Camera.log') - genesets = c() - if (bigmt > "") - { - bigenesets = readLines(bigmt) - genesets = bigenesets - } - if (histgmt > "") - { - hgenesets = readLines(histgmt) - if (bigmt > "") { - genesets = rbind(genesets,hgenesets) - } else { - genesets = hgenesets - } # use only history if no bi - } - print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt)) - genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n - outf = outfname - head=paste(myTitle,'edgeR GSEA') - write(head,file=outfname,append=F) - ntest=length(genesets) - urownames = toupper(rownames(y)) - upcam = c() - downcam = c() - for (i in 1:ntest) { - gs = unlist(genesets[i]) - g = gs[1] # geneset_id - u = gs[2] - if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") } - glist = gs[3:length(gs)] # member gene symbols - glist = toupper(glist) - inglist = urownames %in% glist - nin = sum(inglist) - if ((nin > minnin) && (nin < maxnin)) { - ### print(paste('@@found',sum(inglist),'genes in glist')) - camres = camera(y=y,index=inglist,design=design) - if (! is.null(camres)) { - rownames(camres) = g # gene set name - camres = cbind(GeneSet=g,URL=u,camres) - if (camres\$Direction == "Up") - { - upcam = rbind(upcam,camres) } else { - downcam = rbind(downcam,camres) - } - } - } - } - uscam = upcam[order(upcam\$PValue),] - unadjp = uscam\$PValue - uscam\$adjPValue = p.adjust(unadjp,method=fdrtype) - nup = max(10,sum((uscam\$adjPValue < fdrthresh))) - dscam = downcam[order(downcam\$PValue),] - unadjp = dscam\$PValue - dscam\$adjPValue = p.adjust(unadjp,method=fdrtype) - ndown = max(10,sum((dscam\$adjPValue < fdrthresh))) - write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F) - write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F) - print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:')) - write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F) - print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:')) - write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F) - sink() -} - - - - -doGSEA = function(y=NULL,design=NULL,histgmt="", - bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", - ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH") -{ - sink('Camera.log') - genesets = c() - if (bigmt > "") - { - bigenesets = readLines(bigmt) - genesets = bigenesets - } - if (histgmt > "") - { - hgenesets = readLines(histgmt) - if (bigmt > "") { - genesets = rbind(genesets,hgenesets) - } else { - genesets = hgenesets - } # use only history if no bi - } - print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt)) - genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n - outf = outfname - head=paste(myTitle,'edgeR GSEA') - write(head,file=outfname,append=F) - ntest=length(genesets) - urownames = toupper(rownames(y)) - upcam = c() - downcam = c() - incam = c() - urls = c() - gsids = c() - for (i in 1:ntest) { - gs = unlist(genesets[i]) - gsid = gs[1] # geneset_id - url = gs[2] - if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") } - glist = gs[3:length(gs)] # member gene symbols - glist = toupper(glist) - inglist = urownames %in% glist - nin = sum(inglist) - if ((nin > minnin) && (nin < maxnin)) { - incam = c(incam,inglist) - gsids = c(gsids,gsid) - urls = c(urls,url) - } - } - incam = as.list(incam) - names(incam) = gsids - allcam = camera(y=y,index=incam,design=design) - allcamres = cbind(geneset=gsids,allcam,URL=urls) - for (i in 1:ntest) { - camres = allcamres[i] - res = try(test = (camres\$Direction == "Up")) - if ("try-error" %in% class(res)) { - cat("test failed, camres = :") - print.noquote(camres) - } else { if (camres\$Direction == "Up") - { upcam = rbind(upcam,camres) - } else { downcam = rbind(downcam,camres) - } - - } - } - uscam = upcam[order(upcam\$PValue),] - unadjp = uscam\$PValue - uscam\$adjPValue = p.adjust(unadjp,method=fdrtype) - nup = max(10,sum((uscam\$adjPValue < fdrthresh))) - dscam = downcam[order(downcam\$PValue),] - unadjp = dscam\$PValue - dscam\$adjPValue = p.adjust(unadjp,method=fdrtype) - ndown = max(10,sum((dscam\$adjPValue < fdrthresh))) - write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F) - write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F) - print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:')) - write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F) - print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:')) - write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F) - sink() - } - - -edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, - fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F, - filterquantile=0.2, subjects=c(),mydesign=NULL, - doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19', - histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", - doCook=F,DESeq_fitType="parameteric") -{ - # Error handling - if (length(unique(group))!=2){ - print("Number of conditions identified in experiment does not equal 2") - q() - } - require(edgeR) - options(width = 512) - mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ") - allN = nrow(Count_Matrix) - nscut = round(ncol(Count_Matrix)/2) - colTotmillionreads = colSums(Count_Matrix)/1e6 - counts.dataframe = as.data.frame(c()) - rawrs = rowSums(Count_Matrix) - nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes - nzN = nrow(nonzerod) - nzrs = rowSums(nonzerod) - zN = allN - nzN - print('# Quantiles for non-zero row counts:',quote=F) - print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F) - if (useNDF == T) - { - gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut - lo = colSums(Count_Matrix[!gt1rpin3,]) - workCM = Count_Matrix[gt1rpin3,] - cleanrs = rowSums(workCM) - cleanN = length(cleanrs) - meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="") - print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F) - maint = paste('Filter >=1/million reads in >=',nscut,'samples') - } else { - useme = (nzrs > quantile(nzrs,filterquantile)) - workCM = nonzerod[useme,] - lo = colSums(nonzerod[!useme,]) - cleanrs = rowSums(workCM) - cleanN = length(cleanrs) - meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="") - print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F) - maint = paste('Filter below',filterquantile,'quantile') - } - cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle) - allgenes = rownames(workCM) - reg = "^chr([0-9]+):([0-9]+)-([0-9]+)" - genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/" - ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='') - testreg = str_match(allgenes,reg) - if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string - { - print("@@ using ucsc substitution for urls") - contigurls = paste0(ucsc,"&position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>") - } else { - print("@@ using genecards substitution for urls") - contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>") - } - print.noquote("# urls") - print.noquote(head(contigurls)) - print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) - cmrowsums = rowSums(workCM) - TName=unique(group)[1] - CName=unique(group)[2] - if (is.null(mydesign)) { - if (length(subjects) == 0) - { - mydesign = model.matrix(~group) - } - else { - subjf = factor(subjects) - mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it - } - } - print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=','))) - print.noquote('Using design matrix:') - print.noquote(mydesign) - if (doedgeR) { - sink('edgeR.log') - #### Setup DGEList object - DGEList = DGEList(counts=workCM, group = group) - DGEList = calcNormFactors(DGEList) - - DGEList = estimateGLMCommonDisp(DGEList,mydesign) - comdisp = DGEList\$common.dispersion - DGEList = estimateGLMTrendedDisp(DGEList,mydesign) - if (edgeR_priordf > 0) { - print.noquote(paste("prior.df =",edgeR_priordf)) - DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf) - } else { - DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) - } - DGLM = glmFit(DGEList,design=mydesign) - DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed - efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors - normData = (1e+06*DGEList\$counts/efflib) - uoutput = cbind( - Name=as.character(rownames(DGEList\$counts)), - DE\$table, - adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), - Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData, - DGEList\$counts - ) - soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable - goodness = gof(DGLM, pcutoff=fdrthresh) - if (sum(goodness\$outlier) > 0) { - print.noquote('GLM outliers:') - print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F) - } else { - print('No GLM fit outlier genes found\n') - } - z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2) - pdf("edgeR_GoodnessofFit.pdf") - qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion") - abline(0,1,lwd=3) - points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon") - dev.off() - estpriorn = getPriorN(DGEList) - print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F) - efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors - normData = (1e+06*DGEList\$counts/efflib) - uniqueg = unique(group) - #### Plot MDS - sample_colors = match(group,levels(group)) - sampleTypes = levels(factor(group)) - print.noquote(sampleTypes) - pdf("edgeR_MDSplot.pdf") - plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors) - legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19) - grid(col="blue") - dev.off() - colnames(normData) = paste( colnames(normData),'N',sep="_") - print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=','))) - nzd = data.frame(log(nonzerod + 1e-2,10)) - try( boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") ) - write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F) - tt = cbind( - Name=as.character(rownames(DGEList\$counts)), - DE\$table, - adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), - Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums - ) - print.noquote("# edgeR Top tags\n") - tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely - tt = tt[order(DE\$table\$PValue),] - print.noquote(tt[1:50,]) - deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,]) - nsig = length(deTags) - print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F) - deColours = ifelse(deTags,'red','black') - pdf("edgeR_BCV_vs_abundance.pdf") - plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance") - dev.off() - dg = DGEList[order(DE\$table\$PValue),] - #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg))) - efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors - normData = (1e+06*dg\$counts/efflib) - outpdfname="edgeR_top_100_heatmap.pdf" - hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle)) - outSmear = "edgeR_smearplot.pdf" - outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='') - smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain) - qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf') - norm.factor = DGEList\$samples\$norm.factors - topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ] - edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR)) - edgeRcounts = rep(0, length(allgenes)) - edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits - sink() - } ### doedgeR - if (doDESeq2 == T) - { - sink("DESeq2.log") - # DESeq2 - require('DESeq2') - library('RColorBrewer') - if (length(subjects) == 0) - { - pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM)) - deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx)) - } else { - pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM)) - deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx)) - } - #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype) - #rDESeq = results(DESeq2) - #newCountDataSet(workCM, group) - deSeqDatsizefac = estimateSizeFactors(deSEQds) - deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType) - resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype) - rDESeq = as.data.frame(results(resDESeq)) - rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls) - srDESeq = rDESeq[order(rDESeq\$pvalue),] - qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf') - cat("# DESeq top 50\n") - print.noquote(srDESeq[1:50,]) - write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F) - topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ] - DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq)) - DESeqcounts = rep(0, length(allgenes)) - DESeqcounts[DESeqcountsindex] = 1 - pdf("DESeq2_dispersion_estimates.pdf") - plotDispEsts(resDESeq) - dev.off() - ysmall = abs(min(rDESeq\$log2FoldChange)) - ybig = abs(max(rDESeq\$log2FoldChange)) - ylimit = min(4,ysmall,ybig) - pdf("DESeq2_MA_plot.pdf") - plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit)) - dev.off() - rlogres = rlogTransformation(resDESeq) - sampledists = dist( t( assay(rlogres) ) ) - sdmat = as.matrix(sampledists) - pdf("DESeq2_sample_distance_plot.pdf") - heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"), - col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) - dev.off() - ###outpdfname="DESeq2_top50_heatmap.pdf" - ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle)) - sink() - result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) ) - if ("try-error" %in% class(result)) { - print.noquote('DESeq2 plotPCA failed.') - } else { - pdf("DESeq2_PCA_plot.pdf") - #### wtf - print? Seems needed to get this to work - print(ppca) - dev.off() - } - } - - if (doVoom == T) { - sink('VOOM.log') - if (doedgeR == F) { - #### Setup DGEList object - DGEList = DGEList(counts=workCM, group = group) - DGEList = calcNormFactors(DGEList) - DGEList = estimateGLMCommonDisp(DGEList,mydesign) - DGEList = estimateGLMTrendedDisp(DGEList,mydesign) - DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) - DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) - norm.factor = DGEList\$samples\$norm.factors - } - pdf("VOOM_mean_variance_plot.pdf") - dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor) - dev.off() - # Use limma to fit data - fit = lmFit(dat.voomed, mydesign) - fit = eBayes(fit) - rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none") - qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='VOOM_qqplot.pdf') - rownames(rvoom) = rownames(workCM) - rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls) - srvoom = rvoom[order(rvoom\$P.Value),] - cat("# VOOM top 50\n") - print(srvoom[1:50,]) - write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F) - # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma - topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ] - voomcountsindex = which(allgenes %in% topresults.voom\$ID) - voomcounts = rep(0, length(allgenes)) - voomcounts[voomcountsindex] = 1 - sink() - } - - if (doCamera) { - doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle, - outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype) - } - - if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) { - if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) { - vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh) - counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, - VOOM_limma = voomcounts, row.names = allgenes) - } else if ((doDESeq2==T) && (doedgeR==T)) { - vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh) - counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes) - } else if ((doVoom==T) && (doedgeR==T)) { - vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh) - counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes) - } - - if (nrow(counts.dataframe > 1)) { - counts.venn = vennCounts(counts.dataframe) - vennf = "Venn_significant_genes_overlap.pdf" - pdf(vennf) - vennDiagram(counts.venn,main=vennmain,col="maroon") - dev.off() - } - } #### doDESeq2 or doVoom - -} -#### Done - -###sink(stdout(),append=T,type="message") -builtin_gmt = "" -history_gmt = "" -history_gmt_name = "" -out_edgeR = F -out_DESeq2 = F -out_VOOM = "$out_VOOM" -doDESeq2 = $DESeq2.doDESeq2 # make these T or F -doVoom = $doVoom -doCamera = $camera.doCamera -doedgeR = $edgeR.doedgeR -edgeR_priordf = 0 - - -#if $doVoom == "T": - out_VOOM = "$out_VOOM" -#end if - -#if $DESeq2.doDESeq2 == "T": - out_DESeq2 = "$out_DESeq2" - DESeq_fitType = "$DESeq2.DESeq_fitType" -#end if - -#if $edgeR.doedgeR == "T": - out_edgeR = "$out_edgeR" - edgeR_priordf = $edgeR.edgeR_priordf -#end if - -#if $camera.doCamera == 'T' - #if $camera.gmtSource.refgmtSource == "indexed" or $camera.gmtSource.refgmtSource == "both": - builtin_gmt = "${camera.gmtSource.builtinGMT.fields.path}" - #end if - #if $camera.gmtSource.refgmtSource == "history" or $camera.gmtSource.refgmtSource == "both": - history_gmt = "${camera.gmtSource.ownGMT}" - history_gmt_name = "${camera.gmtSource.ownGMT.name}" - #end if -#end if - - -if (sum(c(doedgeR,doVoom,doDESeq2)) == 0) -{ -write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr()) -quit(save="no",status=2) -} - -Out_Dir = "$html_file.files_path" -Input = "$input1" -TreatmentName = "$treatment_name" -TreatmentCols = "$Treat_cols" -ControlName = "$control_name" -ControlCols= "$Control_cols" -org = "$input1.dbkey" -if (org == "") { org = "hg19"} -fdrtype = "$fdrtype" -fdrthresh = $fdrthresh -useNDF = $useNDF -fQ = $fQ # non-differential centile cutoff -myTitle = "$title" -sids = strsplit("$subjectids",',') -subjects = unlist(sids) -nsubj = length(subjects) -TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1 -CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 -cat('Got TCols=') -cat(TCols) -cat('; CCols=') -cat(CCols) -cat('\n') -useCols = c(TCols,CCols) -if (file.exists(Out_Dir) == F) dir.create(Out_Dir) -Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header -snames = colnames(Count_Matrix) -nsamples = length(snames) -if (nsubj > 0 & nsubj != nsamples) { -options("show.error.messages"=T) -mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','), - 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=',')) -write(mess, stderr()) -quit(save="no",status=4) -} -if (length(subjects) != 0) {subjects = subjects[useCols]} -Count_Matrix = Count_Matrix[,useCols] ### reorder columns -rn = rownames(Count_Matrix) -islib = rn %in% c('librarySize','NotInBedRegions') -LibSizes = Count_Matrix[subset(rn,islib),][1] # take first -Count_Matrix = Count_Matrix[subset(rn,! islib),] -group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor -group = factor(group, levels=c(ControlName,TreatmentName)) -colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns -results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2, - fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.', - myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects, - doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org, - histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType) -sessionInfo() -]]> -</configfile> -</configfiles> -<help> - -**What it does** - -Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes. -Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design. - -**Input** - -Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper -and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the -non-negative integer count of reads from one sample overlapping the feature. -The matrix must have a header row uniquely identifying the source samples, and unique row names in -the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods. - -**Specifying comparisons** - -This is basically dumbed down for two factors - case vs control. - -More complex interfaces are possible but painful at present. -Probably need to specify a phenotype file to do this better. -Work in progress. Send code. - -If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples), -put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or -A list of integers, one for each subject or an empty string if samples are all independent. -If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix. -Integers for samples that are not in the analysis *must* be present in the string as filler even if not used. - -So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones -eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use -8,9,1,1,2,2 -as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6 - -**Methods available** - -You can run 3 popular Bioconductor packages available for count data. - -edgeR - see edgeR_ for details - -VOOM/limma - see limma_VOOM_ for details - -DESeq2 - see DESeq2_ for details - -and optionally camera in edgeR which works better if MSigDB is installed. - -**Outputs** - -Some helpful plots and analysis results. Note that most of these are produced using R code -suggested by the excellent documentation and vignettes for the Bioconductor -packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy. - -**Note on Voom** - -The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method. - -This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma. - -voom is an acronym for mean-variance modelling at the observational level. -The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation. -Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend. -This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance. -The weights are then used in the linear modelling process to adjust for heteroscedasticity. - -In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess. -The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag. -The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag. -Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays. -Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation. -This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data. - - -Author(s) - -Charity Law and Gordon Smyth - -References - -Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia. - -Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts. -Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia. -http://www.statsci.org/smyth/pubs/VoomPreprint.pdf - -See Also - -A voom case study is given in the edgeR User's Guide. - -vooma is a similar function but for microarrays instead of RNA-seq. - - -***old rant on changes to Bioconductor package variable names between versions*** - -The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) -breaking this and all other code that assumed the old name for this variable, -between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). -This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing -to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly -when their old scripts break. This tool currently now works with 2.4.6. - -**Note on prior.N** - -http://seqanswers.com/forums/showthread.php?t=5591 says: - -*prior.n* - -The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. -You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood -in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your -tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the -common likelihood the weight of one observation. - -In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, -or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that -you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation -(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? -What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. -If you have more samples, then the tagwise dispersion estimates will be more reliable, -so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. - - -From Bioconductor Digest, Vol 118, Issue 5, Gordon writes: - -Dear Dorota, - -The important settings are prior.df and trend. - -prior.n and prior.df are related through prior.df = prior.n * residual.df, -and your experiment has residual.df = 36 - 12 = 24. So the old setting of -prior.n=10 is equivalent for your data to prior.df = 240, a very large -value. Going the other way, the new setting of prior.df=10 is equivalent -to prior.n=10/24. - -To recover old results with the current software you would use - - estimateTagwiseDisp(object, prior.df=240, trend="none") - -To get the new default from old software you would use - - estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE) - -Actually the old trend method is equivalent to trend="loess" in the new -software. You should use plotBCV(object) to see whether a trend is -required. - -Note you could also use - - prior.n = getPriorN(object, prior.df=10) - -to map between prior.df and prior.n. - ----- - -**Attributions** - -edgeR - edgeR_ - -VOOM/limma - limma_VOOM_ - -DESeq2 - DESeq2_ for details - -See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package. - -Galaxy_ (that's what you are using right now!) for gluing everything together - -Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is -licensed to you under the LGPL_ like other rgenetics artefacts - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html -.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html -.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html -.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html -.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html -.. _Galaxy: http://getgalaxy.org -</help> - -</tool> - - This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/2c281898882a/ Changeset: 2c281898882a User: fubar Date: 2013-10-08 01:52:21 Summary: backout -r 10800 Affected #: 4 files diff -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 -r 2c281898882a3c35713166e489667fe084ce5413 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -109,7 +109,6 @@ self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) ) - self.use_data_id_on_string = string_as_bool( kwargs.get( "use_data_id_on_string", "False" ) ) self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] diff -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 -r 2c281898882a3c35713166e489667fe084ce5413 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -1,6 +1,5 @@ import os import galaxy.tools -import re from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation @@ -192,20 +191,14 @@ data = data.to_history_dataset_association( None ) inp_data[name] = data -# else: # HDA -# if data.hid: -# input_names.append( 'data %s' % data.hid ) + else: # HDA + if data.hid: + input_names.append( 'data %s' % data.hid ) input_ext = data.ext if data.dbkey not in [None, '?']: input_dbkey = data.dbkey - data_name_sane = re.sub('[^a-zA-Z0-9_]+', '', data.name) - if not trans.app.config.use_data_id_on_string: - # we want names in our on_strings not numbers - input_names.append(data_name_sane) - else: - if data.hid: - input_names.append('data %s' % data.hid) + # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} db_dataset = trans.db_dataset_for( input_dbkey ) @@ -239,14 +232,11 @@ if len( input_names ) == 1: on_text = input_names[0] elif len( input_names ) == 2: - #on_text = '%s and %s' % tuple(input_names[0:2]) - on_text = '%s_%s' % tuple(input_names[0:2]) + on_text = '%s and %s' % tuple(input_names[0:2]) elif len( input_names ) == 3: - #on_text = '%s, %s, and %s' % tuple(input_names[0:3]) - on_text = '%s_%s_%s' % tuple(input_names[0:3]) + on_text = '%s, %s, and %s' % tuple(input_names[0:3]) elif len( input_names ) > 3: - #on_text = '%s, %s, and others' % tuple(input_names[0:2]) - on_text = '%s_%s_and_others' % tuple(input_names[0:2]) + on_text = '%s, %s, and others' % tuple(input_names[0:2]) else: on_text = "" # Add the dbkey to the incoming parameters diff -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 -r 2c281898882a3c35713166e489667fe084ce5413 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -273,19 +273,19 @@ </stdio><outputs> - <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"> + <data format="tabular" name="fusions" label="${on_string}_tophat2fus.xls" from_work_dir="tophat_out/fusions.out"><filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data> - <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> + <data format="bed" name="insertions" label="${on_string}_tophat2ins.bed" from_work_dir="tophat_out/insertions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> + <data format="bed" name="deletions" label="${on_string}_tophhat2del.bed" from_work_dir="tophat_out/deletions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"> + <data format="bed" name="junctions" label="${on_string}tophat2sj.bed" from_work_dir="tophat_out/junctions.bed"><expand macro="dbKeyActions" /></data> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"> + <data format="bam" name="accepted_hits" label="${on_string}tophat2hits.bam" from_work_dir="tophat_out/accepted_hits.bam"><expand macro="dbKeyActions" /></data></outputs> diff -r 962d981799cf7db1fbc5dbd0e964a93771703bb7 -r 2c281898882a3c35713166e489667fe084ce5413 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -113,6 +113,8 @@ </stdio><inputs> + <param name="jobtitle" type="text" value="bowtie2" label="Memorable short reminder of this job's importance for outputs" /> + <conditional name="library"><param name="type" type="select" label="Is this library mate-paired?"> @@ -216,7 +218,7 @@ <outputs> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_{jobtitle}_unaligL.fastq" ><filter>unaligned_file is True</filter><actions><action type="format"> @@ -224,7 +226,7 @@ </action></actions></data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_{jobtitle}_unaligR.fastq)"><filter>library['type'] == "paired" and unaligned_file is True</filter><actions><action type="format"> @@ -232,7 +234,7 @@ </action></actions></data> - <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}_{jobtitle}_aligned.bam"><actions><conditional name="reference_genome.source"><when value="indexed"> https://bitbucket.org/galaxy/galaxy-central/commits/6a39fac59cc0/ Changeset: 6a39fac59cc0 User: fubar Date: 2013-10-08 01:53:45 Summary: backout -r 10802 Affected #: 2 files diff -r 2c281898882a3c35713166e489667fe084ce5413 -r 6a39fac59cc0cd2d0485ec5c6d5af273e8b7d78d lib/galaxy/tools/parameters/output.py --- a/lib/galaxy/tools/parameters/output.py +++ b/lib/galaxy/tools/parameters/output.py @@ -65,7 +65,7 @@ def is_case( self, output_dataset, other_values ): ref = self.get_ref( output_dataset, other_values ) return bool( str( ref ) == self.value ) - + class DatatypeIsInstanceToolOutputActionConditionalWhen( ToolOutputActionConditionalWhen ): tag = "when datatype_isinstance" def __init__( self, parent, config_elem, value ): @@ -215,11 +215,12 @@ self.offset = elem.get( 'offset', -1 ) self.offset = int( self.offset ) else: + self.options = [] self.missing_tool_data_table_name = self.name def get_value( self, other_values ): - try: + if self.options: options = self.options - except: + else: options = [] for filter in self.filters: options = filter.filter_options( options, other_values ) @@ -248,7 +249,7 @@ def __init__( self, parent, elem ): super( FormatToolOutputAction, self ).__init__( parent, elem ) self.default = elem.get( 'default', None ) - + def apply_action( self, output_dataset, other_values ): value = self.option.get_value( other_values ) if value is None and self.default is not None: @@ -431,7 +432,7 @@ value = str( getattr( ref.metadata, self.name ) ) rval = [] for fields in options: - if self.keep == ( self.compare( fields[self.column], value ) ): + if self.keep == ( self.compare( fields[self.column], value ) ): rval.append( fields ) return rval @@ -452,7 +453,7 @@ value = self.cast( value ) except: value = False #unable to cast or access value; treat as false - if self.keep == bool( value ): + if self.keep == bool( value ): rval.append( fields ) return rval @@ -480,7 +481,7 @@ option_types = {} for option_type in [ NullToolOutputActionOption, FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption ]: option_types[ option_type.tag ] = option_type - + filter_types = {} for filter_type in [ ParamValueToolOutputActionOptionFilter, InsertColumnToolOutputActionOptionFilter, MultipleSplitterFilter, ColumnStripFilter, MetadataValueFilter, BooleanFilter, StringFunctionFilter, ColumnReplaceFilter ]: filter_types[ filter_type.tag ] = filter_type @@ -524,5 +525,5 @@ def compare_re_search( value1, value2 ): #checks pattern=value2 in value1 return bool( re.search( value2, value1 ) ) - + compare_types = { 'eq':compare_eq, 'neq':compare_neq, 'gt':compare_gt, 'gte':compare_gte, 'lt':compare_lt, 'lte':compare_lte, 'in':compare_in, 'startswith':compare_startswith, 'endswith':compare_endswith, "re_search":compare_re_search } diff -r 2c281898882a3c35713166e489667fe084ce5413 -r 6a39fac59cc0cd2d0485ec5c6d5af273e8b7d78d tool-data/bowtie2_indices.loc.sample --- a/tool-data/bowtie2_indices.loc.sample +++ b/tool-data/bowtie2_indices.loc.sample @@ -1,37 +1,37 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie2 indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. # -#<unique_build_id><dbkey><display_name><file_base_path> +# <unique_build_id><dbkey><display_name><file_base_path> # -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie2/hg18/, -#then the bowtie2_indices.loc entry would look like this: +# So, for example, if you had hg18 indexes stored in: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# /depot/data2/galaxy/hg19/bowtie2/ # -#and your /depot/data2/galaxy/bowtie2/hg18/ directory -#would contain hg18.*.ebwt files: +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... +# then the bowtie2_indices.loc entry could look like this: # -#Your bowtie2_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 -#...etc... +#More examples: # -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 # +# https://bitbucket.org/galaxy/galaxy-central/commits/99be46d34966/ Changeset: 99be46d34966 User: fubar Date: 2013-10-08 01:54:45 Summary: backout -r 10806 Affected #: 1 file diff -r 6a39fac59cc0cd2d0485ec5c6d5af273e8b7d78d -r 99be46d34966236412d0cf69198143ce71a8958d tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -87,23 +87,22 @@ ## read group information #if str($read_group.selection) == "yes": #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm: - --rg-id $read_group.rgid - --rg LB:$read_group.rglb - --rg PL:$read_group.rgpl - --rg SM:$read_group.rgsm + --rg-id "$read_group.rgid" + --rg "LB:$read_group.rglb" + --rg "PL:$read_group.rgpl" + --rg "SM:$read_group.rgsm" #end if #end if ## view/sort and output file - | samtools view -Su - | samtools sort -o - - > $output; + | samtools view -Su - | samtools sort -o - - > $output ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - - mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r; + ;mv $left $output_unaligned_reads_l; + mv $right $output_unaligned_reads_r #end if </command> @@ -218,7 +217,7 @@ <outputs> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_{jobtitle}_unaligL.fastq" > + <data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_${jobtitle}_unaligL.fastq" ><filter>unaligned_file is True</filter><actions><action type="format"> @@ -226,7 +225,7 @@ </action></actions></data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_{jobtitle}_unaligR.fastq)"> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_${jobtitle}_unaligR.fastq)"><filter>library['type'] == "paired" and unaligned_file is True</filter><actions><action type="format"> @@ -234,7 +233,7 @@ </action></actions></data> - <data format="bam" name="output" label="${tool.name} on ${on_string}_{jobtitle}_aligned.bam"> + <data format="bam" name="output" label="${tool.name} on ${on_string}_${jobtitle}_aligned.bam"><actions><conditional name="reference_genome.source"><when value="indexed"> @@ -256,6 +255,17 @@ </outputs><tests> + <test> +  + <param name="type" value="single"/> + <param name="selection" value="no"/> + <param name="full" value="no"/> + <param name="unaligned_file" value="false"/> + <param name="source" value="history" /> + <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/> + <param name="own_file" value="bowtie2/phix_genome.fasta" /> + <output name="output" file="bowtie2/phix_mapped.bam" /> + </test></tests><help> https://bitbucket.org/galaxy/galaxy-central/commits/99404250db29/ Changeset: 99404250db29 User: fubar Date: 2013-10-08 01:55:24 Summary: backout -r 10808 Affected #: 3 files diff -r 99be46d34966236412d0cf69198143ce71a8958d -r 99404250db290eafa86f1e97e13100d9f705284a lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -1,5 +1,6 @@ import os import galaxy.tools +import re from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation @@ -191,14 +192,20 @@ data = data.to_history_dataset_association( None ) inp_data[name] = data - else: # HDA - if data.hid: - input_names.append( 'data %s' % data.hid ) +# else: # HDA +# if data.hid: +# input_names.append( 'data %s' % data.hid ) input_ext = data.ext if data.dbkey not in [None, '?']: input_dbkey = data.dbkey - + data_name_sane = re.sub('[^a-zA-Z0-9_]+', '', data.name) + if trans.app.config.use_data_id_on_string: + # we want names in our on_strings not numbers + input_names.append(data_name_sane) + else: + if data.hid: + input_names.append('data %s' % data.hid) # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} db_dataset = trans.db_dataset_for( input_dbkey ) @@ -232,11 +239,14 @@ if len( input_names ) == 1: on_text = input_names[0] elif len( input_names ) == 2: - on_text = '%s and %s' % tuple(input_names[0:2]) + #on_text = '%s and %s' % tuple(input_names[0:2]) + on_text = '%s_%s' % tuple(input_names[0:2]) elif len( input_names ) == 3: - on_text = '%s, %s, and %s' % tuple(input_names[0:3]) + #on_text = '%s, %s, and %s' % tuple(input_names[0:3]) + on_text = '%s_%s_%s' % tuple(input_names[0:3]) elif len( input_names ) > 3: - on_text = '%s, %s, and others' % tuple(input_names[0:2]) + #on_text = '%s, %s, and others' % tuple(input_names[0:2]) + on_text = '%s_%s_and_others' % tuple(input_names[0:2]) else: on_text = "" # Add the dbkey to the incoming parameters diff -r 99be46d34966236412d0cf69198143ce71a8958d -r 99404250db290eafa86f1e97e13100d9f705284a scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -454,5 +454,4 @@ return 1 if __name__ == "__main__": - print '\n\n\n\n#### SGE_ROOT=', os.environ.get('SGE_ROOT','##### no SGE_ROOT!'),'\n\n\n' sys.exit( main() ) diff -r 99be46d34966236412d0cf69198143ce71a8958d -r 99404250db290eafa86f1e97e13100d9f705284a tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,7 +1,6 @@ <?xml version="1.0"?><toolbox><section name="Get Data" id="getext"> - <tool file="rlGAT/rlGAT.xml"/><tool file="data_source/upload.xml"/><tool file="data_source/ucsc_tablebrowser.xml" /><tool file="data_source/ucsc_tablebrowser_test.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/68b694a22c59/ Changeset: 68b694a22c59 User: fubar Date: 2013-10-08 01:56:03 Summary: backout -r 10811 Affected #: 2 files diff -r 99404250db290eafa86f1e97e13100d9f705284a -r 68b694a22c59b6419a568330bbd0a02186068526 run.sh --- a/run.sh +++ b/run.sh @@ -1,6 +1,7 @@ #!/bin/sh cd `dirname $0` + python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 diff -r 99404250db290eafa86f1e97e13100d9f705284a -r 68b694a22c59b6419a568330bbd0a02186068526 tool-data/shared/ucsc/ucsc_build_sites.txt --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt @@ -1,6 +1,8 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn -main http://genome.ucsc.edu/cgi-bin/hgTracks? latCha1,eriEur1,petMar2,papAnu2,ce6,anoCar2,ce2,rn3,loxAfr3,rn5,rn4,droYak1,oreNil2,droYak2,dp3,dp2,vicPac1,vicPac2,caeRem2,caeRem3,geoFor1,sorAra1,caePb2,gadMor1,droAna1,droAna2,triMan1,sacCer2,sacCer3,oryCun2,dasNov3,droGri1,caeJap1,anoCar1,choHof1,taeGut1,sacCer1,tupBel1,ce4,macEug2,ochPri2,gorGor3,mm8,mm7,pteVam1,micMur1,galGal3,galGal2,proCap1,ornAna1,sarHar1,equCab2,equCab1,myoLuc2,rheMac3,rheMac2,droPer1,apiMel1,droVir2,droVir1,cerSim1,dm1,ailMel1,cb3,calJac1,calJac3,melUnd1,droSim1,hg16,hg17,hg18,hg19,monDom5,monDom4,oviAri1,petMar1,oviAri3,droSec1,saiBol1,aplCal1,strPur1,mm9,braFlo1,oryLat2,susScr2,susScr3,canFam1,canFam3,canFam2,echTel2,caePb1,echTel1,ci2,ci1,dm3,papHam1,ponAbe2,ce10,mm10,xenTro1,xenTro3,xenTro2,fr3,fr2,fr1,galGal4,gasAcu1,dm2,nomLeu3,nomLeu2,nomLeu1,apiMel2,priPac1,cavPor3,panTro4,panTro1,panTro3,panTro2,danRer7,danRer6,danRer5,danRer4,danRer3,dipOrd1,tetNig2,tetNig1,droMoj2,bosTau3,bosTau2,bosTau4,musFur1,bosTau6,melGal1,droEre1,hetGla2,turTru2,hetGla1,monDom1,cb1,droMoj1,speTri2,allMis1,strPur2,otoGar3,bosTau7,tarSyr1,felCat3,chrPic1,anoGam1,felCat4,felCat5 +main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn -archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? therSibi1,symbTher_IAM14863,haloBori1,zymoMobi_ZM4,therFusc_YX,methIgne1,methPalus1,nocaJS61,his2Viru,acidCryp_JF_5,lactLact,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,jannCCS1,syntFuma_MPOB,dichNodo_VCS1703A,eschColi_O157H7,burk383,alteMacl_ATCC27126,bradJapo,lebron_Phage,aerPer1,acinSp_ADP1,anapMarg_ST_MARIES,sulfIsla_L_D_8_5,desuPsyc_LSV54,sulfIsla_ROD_SHAPED_VIRUS_2,shewDeni,methBoon1,shewLoihPV4,igniHosp1,therTher_HB8,ferrAcid2,sulfIsla_REY15A,acidCell_11B,stapHell1,acidBoon1,salmTyph_LT2,methBurt2,pyroYaya1,haloHisp1,glucOxyd_621H,geobSulf,acidFila_VIRUS_6,soliUsit_ELLIN6076,methAeol1,procMari_CCMP1375,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,therUzon1,peloProp_DSM2379,orieTsut_BORYONG,salmEnte_PARATYPI_ATC,therOnnu1,onioYell_PHYTOPLASMA,mariAqua_VT8,heliPylo_J99,pf5,psycIngr_37,methMahi1,candPela_UBIQUE_HTCC1,myxoXant_DK_1622,salmTyph_TY2,chloChlo_CAD3,mesoFlor_L1,shewW318,pyro1860_1,closDiff_630,pyroFuri_COM1,methMaze1,shewWood,haloPhag_HF2,sulfViru_KAMCHATKA_1,ureaUrea,streCoel,polaJS66,rhodRubr_ATCC11170,rhodRHA1,pireSp,geobBemi_BEM,enteCloa_ATCC13047_uid48363,franTula_TULARENSIS,syneSp_WH8102,archProf1,methPetr_PM1,heliAcin_SHEEBA,thioCrun_XCL_2,haloHalo1,idioLoih_L2TR,xantCamp,sodaGlos_MORSITANS,coryEffi_YS_314,mycoTube_H37RV,polyQLWP,peloLute_DSM273,burkCeno_AU_1054,vibrVuln_CMCP6_1,ente638,neorSenn_MIYAYAMA,burkCepa_AMMD,methMari_C5_1,methZhil1,pyroFuma1,methBark1,geobMeta_GS15,eschColi_CFT073,metMar1,enteFaec_V583,hodgCica_DSEM,erwiCaro_ATROSEPTICA,methFerv1,igniAggr1,campJeju_81_176,pseuHalo_TAC125,chlaTrac,heliPylo_SHI470,chroViol,mycoGeni,methSp_FS406_1,therTher_HB27,sulfIsla_Y_G_57_14,uncuMeth_RCI,haloUtah1,sulfSolf_98_2,propAcne_KPA171202,acidJS42,chroSale_DSM3043,tropWhip_TW08_27,acidFila_VIRUS_2,natrPhar1,salmEnte_CHOLERAESUIS,rubrXyla_DSM9941,methVulc1,franCcI3,persMariEXH1,caldSacc_DSM8903,haloSali1,lactPlan,strePneu_R6_uid57859,siliPome_DSS_3,nitrWino_NB_255,mesoLoti,coxiBurn,acidFila_VIRUS_7,acidBact_ELLIN345,caldMaqu1,acidFila_VIRUS_3,amycMedi_U32,acidFila_VIRUS_1,therAggr1,acidFila_VIRUS_8,acidFila_VIRUS_9,methKand1,methCaps_BATH,burkCeno_HI2424,psycArct_273_4,buchSp,pyroCali1,chloTepi_TLS,bifiLong,picrTorr1,shewANA3,bdelBact,gramFors_KT0803,peloCarb,sulfIsla_ROD_SHAPED_V,haloHF1,sulfViru_STSV1,clavMich_NCPPB_382,baciSubt2,methPhag_PSIM100,therNeut1,saliTrop_CNB_440,campJeju,blocFlor,pastMult,saliRube_DSM13855,carbHydrZ2901,mycoPhag_BPS,halaJeot1,dehaEthe_195,mycoPhag_CORNDOG,pyroAbys_VIRUS_1,shewMR7,shewMR4,desuMuco1,geobUran_RF4,desuRedu_MI_1,methStad1,legiPneu_PHILADELPHIA,methSWAN1,gloeViol,moorTher_ATCC39073,acidRods_VIRUS_1,roseDeni_OCH_114,natrMaga1,xantOryz_MAFF_311018,shewHali,burkXeno_LB400,heliPylo_26695,geobFRC_32,eschColi_K_12_SUBSTR_W3110,haloArch_DL31,leptInte,methEves1,hydrY04A,tricEryt_IMS101,photLumi,peloTher_SI,therKoda1,desuAuda,lawsIntr_PHE_MN1_00,mycoSmeg_MC2_155,therBaro1,methOkin1,metaCupr1,therElon,shewPutrCN32,eschColi_O157H7_EDL93,mariMari_MCS10,methInfe1,shigFlex_2A,magnMagn_AMB_1,sulfIsla_FILAMENTOUS,erytLito_HTCC2594,coryGlut_Bielefeld,pyrAer1,thioDeni_ATCC25259,deinRadi,yersPest_CO92,therVolc1,wolbEndo_OF_DROSOPHIL,acidHosp1,shewSedi_HAW_EB3,vulcMout1,ralsSola,crimd_Phage,natrPhag_PHICH1,neisMeni_Z2491_1,shewPeal,anabVari_ATCC29413,colwPsyc_34H,xantAuto_PY2,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,salmEnte_ENTERITIDIS,metaSedu,mycoPhag_GILES,lactSali_UCC118,pyroOgun2,flavJohn_UW101,mannSucc_MBEL55E,haemSomn_129PT,therTena2,haloXana1,methFerv_DSM2088,koraCryp1,oceaIhey,haloTurk1,haloWals1,baciHalo,hypeButy1,agroTume_C58_UWASH,pyroIsla1,cytoHutc_ATCC33406,nitrEuro,therMari,pyroArse1,nitrMari1,vibrFisc_ES114_1,methJann1,heliPylo_G27,vibrPara1,metAce1,neisGono_FA1090_1,methConc1,chlaPneu_CWL029,strePyog_M1_GAS,haloLacu1,novoArom_DSM12444,eschColi_536,azoaSp_EBN1,sulfToko1,listInno,sulfAcid1,geobTher_NG80_2,sulfSpin_VIRUS_4,arthFB24,porpGing_W83,leifXyli_XYLI_CTCB0,campFetu_82_40,mycoPhag_Firecracker,mycoPhag_Dori,methTher1,nostSp,sphiAlas_RB2256,saccDegr_2_40,bordBron,rickBell_RML369_C,thioDeni_ATCC33889,methSmit1,alkaMeta_QYMF,sulfIsla_M_16_27,halMar1,vermEise_EF01_2,granBeth_CGDNIH1,therPend1,sulfIsla_L_S_2_15,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,pyroSphe_VIRUS,yersPseu_IP32953,woliSucc,caldSubt1,sulfTurr_ICOSAHEDRAL,methMarb1,aquiAeol,acidSacc1,burkPseu_1106A,tremPrin_PCIT,azorCaul2,synePCC6,hydrSp_128_5R1,baumCica_HOMALODISCA,shewBalt,therTeng,alkaEhrl_MLHE_1,sulSol1,eschColi_UTI89,methHung1,desuKamc1,pediPent_ATCC25745,therGamm1,nanEqu1,shewAmaz,hydr3684,desuVulg_HILDENBOROUG,haheChej_KCTC_2396,sulfIsla_Y_N_15_51,candBloc_FLORIDANUS,haloPhag_SH1,candCars_RUDDII,burkMall_ATCC23344,burkViet_G4,acidTwot_VIRUS,methVann1,archFulg1,fusoNucl,heliHepa,sulfViru_1,sulfViru_2,syntAcid_SB,salmTyph,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,syneElon_PCC_7942,haemInfl_KW20,haloHalo_SL1,plasFalc1,rhodSpha_2_4_1,archVene1,rhodPalu_CGA009,stapMari1,sinoMeli,sulfYell_SS_5,archBJ1_VIRUS,bartHens_HOUSTON_1,sulfAzorFu1,methMari_C6,methMari_C7,caulCres,crocWats_WH8501_0,rhodSpha_ATCC17025,magnMC1,rhodFerr_DSM15236,hydrTher1,heliPylo_HPAG1,pyrHor1,acidBott_VIRUS,sulfIsla_M_16_4,actiPleu_L20,paraDeni_PD1222,borrBurg,pseuAeru,methRumi1,methVolt1,cenaSymb1,geobLovl_SZ,pyrFur2,saccEryt_NRRL_2338,vibrChol_MO10_1,methPetr1,pyroNA2,yersPseu_IP31758,ehrlRumi_WELGEVONDEN,methLabrZ_1,vibrVuln_YJ016_1,vulcDist1,sulfIsla_M_14_25,his1Viru,methTherPT1,methFlag_KT,therAcid1,therPetr_RKU_1,shewFrig,photProf_SS9,burkThai_E264,nitrMult_ATCC25196,methMari_XI,neisMeni_FAM18_1,hermArse,haloVolc1,desuHafn_Y51,nocaFarc_IFM10152,anaeDeha_2CP_C,methPalud1,eschColi_APEC_O1,xyleFast,leucMese_ATCC8293,bactThet_VPI_5482,brucMeli,ferrPlac1,ralsEutr_JMP134,sulfViru_RAGGED_HILLS,pyrAby1,mculMari1,dechArom_RCB,stapAure_MU50,methPhag_PSIM2,eschColi_K12,sulfYO3A,haloMuko1,aeroHydr_ATCC7966,ther4557,baciAnth_AMES,shewOnei +archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? punNye1,homIni20,danRer4,amaVit1,latCha1,eriEur1,criGri1,eriEur2,odoRosDiv1,lepWed1,papAnu2,ce6,ce5,anoCar2,ce3,ce2,chiLan1,rn3,loxAfr3,loxAfr2,simHuman,droMoj2,rn5,rn4,haeCon1,tetNig2,oreNil2,droYak2,dp3,dp2,mhcRef,vicPac1,eptFus1,caePb3,vicPac2,strPur2,caeRem3,geoFor1,caeRem1,sorAra1,oviAri1,galGal4,astMex1,musFur1,borEut13,homIni14,gadMor1,cacTus1,cacTus2,cacTus3,oryCun1,sacCer3,oryCun2,micOch1,colLiv1,caeJap3,melInc1,chlSab1,kirRefV3,kirRefV2,choHof1,droSim1,saiBol1,kirRefV5,kirRefV4,octDeg1,centromers1,droGri1,sc1,CHM1,mhcRefnoNs8,mhcRefnoNs9,dasNov2,dasNov3,taeGut1,caeJap4,taeGut2,caeSp71,equCab2,mhcRefnoNs2,mhcRefnoNs3,mhcRefnoNs4,mhcRefnoNs5,tupBel1,hlaRef2,galGal2,caeSp91,ce4,croPor0,bosTau7,bosTau6,ficAlb2,caePb2,panHod1,gorGor3,gorGor2,gorGor1,mayZeb1,mm7,pteVam1,macEug1,loxAfr1,venter1,micMur1,galGal3,mhcRefnoNs6,priPac2,proCap1,priPac1,mhcRefnoNs7,droEre1,sorAra2,mm10Strains1,ornAna1,xipMac1,anaPla1,mmtv,eutHer13,braNey1,droPer1,bioGla0,ce9,sarHar1,mhcRefnoNs,hlaRef3,simHumanMammal,hlaRef1,equCab1,simHumanPrim,cioSav2,myoLuc1,rheMac3,rheMac2,oreNil1,ailMel1,droSec1,canHg12,simRefMam,apiMel1,homIni13,nemVec1,turTru1,sacCer2,droVir2,droVir1,ce7,myoLuc2,repBase0,repBase1,dm1,susScr2,cb3,calJac1,macFas5,calJac3,dm3,triMan1,neoBri1,canFam1,conCri1,caeAng1,hg15,hg16,hg17,hg18,hg19,lotGig0,monDom5,monDom4,euaGli13,pteAle1,panPan1,petMar1,oviAri3,cb4,caeRem2,cioSav1,aplCal0,aplCal1,gliRes13,strPur1,anoCar1,dasNov1,mm9,tetNig1,mm8,braFlo1,oryLat2,caeJap2,braFlo2,lauRas13,susScr1,jacJac1,susScr3,hg19LggInv,caeJap1,canFam3,canFam2,echTel2,caePb1,echTel1,simHumanMam,ci2,ci1,canFamPoodle1,camFer1,papHam1,ce8,cerSim1,capHir1,droMoj1,oryLat1,ponAbe2,ce10,pseHum1,mm10Patch1,calMil0,caeSp111,hapBur1,cheMyd1,hg19Haps,mm10,falciparum,mhcRefnoNs24,mhcRefnoNs23,mhcRefnoNs22,mhcRefnoNs21,mhcRefnoNs20,xenTro1,xenTro3,xenTro2,xenTro7,falPer1,nonAfr13,homPan20,fr3,fr2,fr1,macEug2,caeRem4,gasAcu1,dm2,nomLeu3,nomLeu2,nomLeu1,apiMel2,melHap1,zonAlb1,tupChi1,ecoRef1,ecoRef3,ecoRef2,chrAsi1,ecoRef4,cavPor3,triCas2,panTro4,pelSin1,panTro1,droAna2,panTro3,panTro2,mhcRefnoNs18,mhcRefnoNs19,lepOcu1,hg19Patch10,strPur3,mhcRefnoNs12,mhcRefnoNs13,mhcRefnoNs10,mhcRefnoNs11,mhcRefnoNs16,mhcRefnoNs17,mhcRefnoNs14,mhcRefnoNs15,sacCer1,melUnd1,apaSpi1,danRer6,danRer5,mesAur1,danRer3,dipOrd1,eleEdw1,hg19Patch2,hg19Patch5,droAna1,hg19Patch9,bruMal1,bosTau3,bosTau2,bosTau5,bosTau4,ochPri2,ochPri3,melGal1,petMar2,rodEnt13,oryAfe1,evoSim1,priMat13,hetGla2,turTru2,repeats2,hetGla1,cb2,monDom1,cb1,speTri1,speTri2,catArr1,allMis1,allMis0,plasFalc3D7_2,araMac1,strPur4,otoGar1,otoGar3,kirRef,myoDav1,falChe1,tarSyr1,letCam1,afrOth13,danRer7,takFla1,droYak1,felCat3,orcOrc1,chrPic1,anoGam1,felCat4,felCat5 +test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 +ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 +psu bx main http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 https://bitbucket.org/galaxy/galaxy-central/commits/c2561f65d6f9/ Changeset: c2561f65d6f9 User: fubar Date: 2013-10-08 04:34:54 Summary: revert bowtie2 and tophat2 wrappers Affected #: 2 files diff -r 68b694a22c59b6419a568330bbd0a02186068526 -r c2561f65d6f9d181e76d60d0f7ed60e1ce94c513 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -1,5 +1,5 @@ -<tool id="tophat2" name="Tophat2" version="0.5"> -  +<tool id="tophat2" name="Tophat2" version="0.6"> + <description>Gapped-read mapper for RNA-seq data</description><version_command>tophat2 --version</version_command><requirements> @@ -268,24 +268,25 @@ </inputs><stdio> - <regex match="Exception" source="both" level="fatal" description="Tool exception"/> + <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/><regex match=".*" source="both" level="log" description="tool progress"/></stdio><outputs> - <data format="tabular" name="fusions" label="${on_string}_tophat2fus.xls" from_work_dir="tophat_out/fusions.out"> + <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/> + <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"><filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data> - <data format="bed" name="insertions" label="${on_string}_tophat2ins.bed" from_work_dir="tophat_out/insertions.bed"> + <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="deletions" label="${on_string}_tophhat2del.bed" from_work_dir="tophat_out/deletions.bed"> + <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"><expand macro="dbKeyActions" /></data> - <data format="bed" name="junctions" label="${on_string}tophat2sj.bed" from_work_dir="tophat_out/junctions.bed"> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"><expand macro="dbKeyActions" /></data> - <data format="bam" name="accepted_hits" label="${on_string}tophat2hits.bam" from_work_dir="tophat_out/accepted_hits.bam"> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"><expand macro="dbKeyActions" /></data></outputs> @@ -312,6 +313,7 @@ </actions></macro></macros> + <tests><test> @@ -450,7 +452,8 @@ <help> **Tophat Overview** -TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009). +TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons. Please cite: Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL. TopHat2: accurate alignment +of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013. .. _Tophat: http://tophat.cbcb.umd.edu/ diff -r 68b694a22c59b6419a568330bbd0a02186068526 -r c2561f65d6f9d181e76d60d0f7ed60e1ce94c513 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -95,14 +95,15 @@ #end if ## view/sort and output file - | samtools view -Su - | samtools sort -o - - > $output + | samtools view -Su - | samtools sort -o - - > $output; ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - ;mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r + + mv $left $output_unaligned_reads_l; + mv $right $output_unaligned_reads_r; #end if </command> @@ -112,8 +113,6 @@ </stdio><inputs> - <param name="jobtitle" type="text" value="bowtie2" label="Memorable short reminder of this job's importance for outputs" /> - <conditional name="library"><param name="type" type="select" label="Is this library mate-paired?"> @@ -217,7 +216,7 @@ <outputs> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_${jobtitle}_unaligL.fastq" > + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" ><filter>unaligned_file is True</filter><actions><action type="format"> @@ -225,7 +224,7 @@ </action></actions></data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_${jobtitle}_unaligR.fastq)"> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"><filter>library['type'] == "paired" and unaligned_file is True</filter><actions><action type="format"> @@ -233,7 +232,7 @@ </action></actions></data> - <data format="bam" name="output" label="${tool.name} on ${on_string}_${jobtitle}_aligned.bam"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="reference_genome.source"><when value="indexed"> https://bitbucket.org/galaxy/galaxy-central/commits/a2ffcbc614d4/ Changeset: a2ffcbc614d4 User: fubar Date: 2013-10-08 04:39:22 Summary: restore original tools/actions/__init__.py Affected #: 1 file diff -r c2561f65d6f9d181e76d60d0f7ed60e1ce94c513 -r a2ffcbc614d42f343f4bab09035e771bb50b0dcc lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -1,6 +1,5 @@ import os import galaxy.tools -import re from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation @@ -23,13 +22,13 @@ """ def execute( self, tool, trans, incoming={}, set_output_hid=True ): raise TypeError("Abstract method") - + class DefaultToolAction( object ): """Default tool action is to run an external command""" - + def collect_input_datasets( self, tool, param_values, trans ): """ - Collect any dataset inputs from incoming. Returns a mapping from + Collect any dataset inputs from incoming. Returns a mapping from parameter name to Dataset instance for each tool parameter that is of the DataToolParameter type. """ @@ -118,9 +117,9 @@ def make_dict_copy( from_dict ): """ Makes a copy of input dictionary from_dict such that all values that are dictionaries - result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle - other complex types ( e.g., lists, etc ), but not sure... - Yes, we need to handle lists (and now are)... + result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle + other complex types ( e.g., lists, etc ), but not sure... + Yes, we need to handle lists (and now are)... """ copy_from_dict = {} for key, value in from_dict.items(): @@ -169,11 +168,11 @@ input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) else: input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) - + # Set history. if not history: history = tool.get_default_history_by_trans( trans, create=True ) - + out_data = odict() # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans ) @@ -186,26 +185,20 @@ if not data: data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) continue - + # Convert LDDA to an HDA. if isinstance(data, LibraryDatasetDatasetAssociation): data = data.to_history_dataset_association( None ) inp_data[name] = data - -# else: # HDA -# if data.hid: -# input_names.append( 'data %s' % data.hid ) + + else: # HDA + if data.hid: + input_names.append( 'data %s' % data.hid ) input_ext = data.ext - + if data.dbkey not in [None, '?']: input_dbkey = data.dbkey - data_name_sane = re.sub('[^a-zA-Z0-9_]+', '', data.name) - if trans.app.config.use_data_id_on_string: - # we want names in our on_strings not numbers - input_names.append(data_name_sane) - else: - if data.hid: - input_names.append('data %s' % data.hid) + # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} db_dataset = trans.db_dataset_for( input_dbkey ) @@ -221,13 +214,13 @@ if 'fasta' in custom_build_dict: build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name - + if not chrom_info: # Default to built-in build. chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) incoming[ "chromInfo" ] = chrom_info inp_data.update( db_datasets ) - + # Determine output dataset permission/roles list existing_datasets = [ inp for inp in inp_data.values() if inp ] if existing_datasets: @@ -239,20 +232,17 @@ if len( input_names ) == 1: on_text = input_names[0] elif len( input_names ) == 2: - #on_text = '%s and %s' % tuple(input_names[0:2]) - on_text = '%s_%s' % tuple(input_names[0:2]) + on_text = '%s and %s' % tuple(input_names[0:2]) elif len( input_names ) == 3: - #on_text = '%s, %s, and %s' % tuple(input_names[0:3]) - on_text = '%s_%s_%s' % tuple(input_names[0:3]) + on_text = '%s, %s, and %s' % tuple(input_names[0:3]) elif len( input_names ) > 3: - #on_text = '%s, %s, and others' % tuple(input_names[0:2]) - on_text = '%s_%s_and_others' % tuple(input_names[0:2]) + on_text = '%s, %s, and others' % tuple(input_names[0:2]) else: on_text = "" # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey params = None #wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed - # Keep track of parent / child relationships, we'll create all the + # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] child_dataset_names = set() @@ -268,7 +258,7 @@ if output.parent: parent_to_child_pairs.append( ( output.parent, name ) ) child_dataset_names.add( name ) - ## What is the following hack for? Need to document under what + ## What is the following hack for? Need to document under what ## conditions can the following occur? (james(a)bx.psu.edu) # HACK: the output data has already been created # this happens i.e. as a result of the async controller @@ -289,7 +279,7 @@ ext = input_extension except Exception, e: pass - + #process change_format tags if output.change_format: if params is None: @@ -332,14 +322,14 @@ object_store_id = data.dataset.object_store_id # these will be the same thing after the first output # This may not be neccesary with the new parent/child associations data.designation = name - # Copy metadata from one of the inputs if requested. + # Copy metadata from one of the inputs if requested. if output.metadata_source: data.init_meta( copy_from=inp_data[output.metadata_source] ) else: data.init_meta() # Take dbkey from LAST input data.dbkey = str(input_dbkey) - # Set state + # Set state # FIXME: shouldn't this be NEW until the job runner changes it? data.state = data.states.QUEUED data.blurb = "queued" @@ -361,7 +351,7 @@ params = make_dict_copy( incoming ) wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) data.name = self._get_default_data_name( data, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) - # Store output + # Store output out_data[ name ] = data if output.actions: #Apply pre-job tool-output-dataset actions; e.g. setting metadata, changing format @@ -383,7 +373,7 @@ parent_dataset = out_data[ parent_name ] child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) - # Store data after custom code runs + # Store data after custom code runs trans.sa_session.flush() # Create the job object job = trans.app.model.Job() @@ -464,7 +454,7 @@ for name in inp_data.keys(): dataset = inp_data[ name ] redirect_url = tool.parse_redirect_url( dataset, incoming ) - # GALAXY_URL should be include in the tool params to enable the external application + # GALAXY_URL should be include in the tool params to enable the external application # to send back to the current Galaxy instance GALAXY_URL = incoming.get( 'GALAXY_URL', None ) assert GALAXY_URL is not None, "GALAXY_URL parameter missing in tool config." https://bitbucket.org/galaxy/galaxy-central/commits/3df68022beef/ Changeset: 3df68022beef User: fubar Date: 2013-10-08 07:15:56 Summary: Big cleanup - remove material in tools/rgenetics accidentally added in August when a push was made from a BakerIDI repository - apologies to all. This push will revert all those changes and also removes the old rgenetics SNP tools which are now deprecated. Affected #: 1 file diff -r a2ffcbc614d42f343f4bab09035e771bb50b0dcc -r 3df68022beef2077798ed50a33afb03be75a841a tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -24,10 +24,29 @@ import optparse import shutil import tempfile -from rgutils import getFileString import zipfile import gzip + +def getFileString(fpath, outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath, fpath) + s = '? ?' + if os.path.isfile(fp): + n = float(os.path.getsize(fp)) + if n > 2**20: + size = ' (%1.1f MB)' % (n/2**20) + elif n > 2**10: + size = ' (%1.1f KB)' % (n/2**10) + elif n > 0: + size = ' (%d B)' % (int(n)) + s = '%s %s' % (fpath, size) + return s + + class FastQC(): """wrapper """ https://bitbucket.org/galaxy/galaxy-central/commits/c8b55344e779/ Changeset: c8b55344e779 User: fubar Date: 2013-10-08 07:30:54 Summary: Proper removal of rgenetics deprecated tool wrappers Affected #: 41 files diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/listFiles.py --- a/tools/rgenetics/listFiles.py +++ /dev/null @@ -1,227 +0,0 @@ -#Provides Upload tool with access to list of available files -import glob,sys -import galaxy.app as thisapp -import galaxy.util - -from elementtree.ElementTree import XML - -librepos = '/usr/local/galaxy/data/rg' -myrepos = '/home/rerla/galaxy' -marchinirepos = '/usr/local/galaxy/data/rg/snptest' - -from galaxy.tools.parameters import DataToolParameter - -#Provides Upload tool with access to list of available builds - -builds = [] -#Read build names and keys from galaxy.util -for dbkey, build_name in galaxy.util.dbnames: - builds.append((build_name,dbkey,False)) - -#Return available builds -def get_available_builds(defval='hg18'): - for i,x in enumerate(builds): - if x[1] == defval: - x = list(x) - x[2] = True - builds[i] = tuple(x) - return builds - - - -def get_tabular_cols( input, outformat='gg' ): - """numeric only other than rs for strict genome graphs - otherwise tabular. Derived from galaxy tool source around August 2007 by Ross""" - columns = [] - seenCnames = {} - elems = [] - colnames = ['Col%d' % x for x in range(input.metadata.columns+1)] - strict = (outformat=='gg') - for i, line in enumerate( file ( input.file_name ) ): - if line and not line.startswith( '#' ): - line = line.rstrip('\r\n') - elems = line.split( '\t' ) - - """ - Strict gg note: - Since this tool requires users to select only those columns - that contain numerical values, we'll restrict the column select - list appropriately other than the first column which must be a marker - """ - if len(elems) > 0: - for col in range(1, input.metadata.columns+1): - isFloat = False # short circuit common result - try: - val = float(elems[col-1]) - isFloat = True - except: - val = elems[col-1] - if val: - if i == 0: # header row - colnames[col] = val - if isFloat or (not strict) or (col == 1): # all in if not GG - option = colnames[col] - if not seenCnames.get(option,None): # new - columns.append((option,str(col),False)) - seenCnames[option] = option - #print 'get_tab: %d=%s. Columns=%s' % (i,line,str(columns)) - if len(columns) > 0 and i > 10: - """ - We have our select list built, so we can break out of the outer most for loop - """ - break - if i == 30: - break # Hopefully we never get here... - for option in range(min(5,len(columns))): - (x,y,z) = columns[option] - columns[option] = (x,y,True) - return columns # sorted select options - -def get_marchini_dir(): - """return the filesystem directory for snptest style files""" - return marchinirepos - - -def get_lib_SNPTESTCaCofiles(): - """return a list of file names - without extensions - available for caco studies - These have a common file name with both _1 and _2 suffixes""" - d = get_marchini_dir() - testsuffix = '.gen_1' # glob these - flist = glob.glob('%s/*%s' % (d,testsuffix)) - flist = [x.split(testsuffix)[0] for x in flist] # leaves with a list of file set names - if len(flist) > 0: - dat = [(flist[0],flist[0],True),] - dat += [(x,x,False) for x in flist[1:]] - else: - dat = [('No Marchini CaCo files found in %s - convert some using the Marchini converter tool' % d,'None',True),] - return dat - -def getChropt(): - """return dynamic chromosome select options - """ - c = ['X','Y'] - c += ['%d' % x for x in range(1,23)] - dat = [(x,x,False) for x in c] - x,y,z = dat[3] - dat[3] = (x,y,True) - return dat - - -def get_phecols(fname=''): - """ return a list of phenotype columns for a multi-select list - prototype: - foo = ('fake - not yet implemented','not implemented','False') - dat = [foo for x in range(5)] - return dat - """ - try: - header = file(fname,'r').next().split() - except: - return [('get_phecols unable to open file %s' % fname,'None',False),] - dat = [(x,x,False) for x in header] - return dat - -#Return various kinds of files - -def get_lib_pedfiles(): - dat = glob.glob('%s/ped/*.ped' % librepos) - dat += glob.glob('%s/ped/*.ped' % myrepos) - dat.sort() - if len(dat) > 0: - dat = [x.split('.ped')[0] for x in dat] - dat = [(x,x,'True') for x in dat] - else: - dat = [('No ped files - add some to %s/ped or %s/ped' % (librepos,myrepos),'None',True),] - return dat - -def get_lib_phefiles(): - ext = 'phe' - dat = glob.glob('%s/pheno/*.%s' % (librepos,ext)) - dat += glob.glob('%s/pheno/*.%s' % (myrepos,ext)) - dat.sort() - if len(dat) > 0: - dat = [(x,x,'False') for x in dat] - else: - dat = [('No %s files - add some to %s/pheno or %s/pheno' % (ext,librepos,myrepos),'None',True),] - return dat - -def get_lib_bedfiles(): - dat = glob.glob('%s/plinkbed/*.bed' % librepos) - dat += glob.glob('%s/plinkbed/*.bed' % myrepos) - dat.sort() - if len(dat) > 0: - dat = [x.split('.bed')[0] for x in dat] - dat = [(x,x,False) for x in dat] - else: - dat = [('No bed files - Please import some to %s/plinkbed or %s/plinkbed' % (librepos,myrepos),'None',True),] - return dat - -def get_lib_fbatfiles(): - dat = glob.glob('%s/plinkfbat/*.ped' % librepos) - dat += glob.glob('%s/plinkfbat/*.ped' % myrepos) - dat.sort() - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No fbat bed files - Please import some to %s/plinkfbat or %s/plinkfbat' % (librepos,myrepos),'None',True),] - return dat - -def get_lib_mapfiles(): - dat = glob.glob('%s/ped/*.map' % librepos) - dat += glob.glob('%s/ped/*.map' % myrepos) - dat.sort() - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No map files - add some to %s/ped' % librepos,'None',True),] - return dat - -def get_my_pedfiles(): - dat = glob.glob('%s/*.ped' % myrepos) - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - -def get_my_mapfiles(): - dat = glob.glob('%s/*.map' % myrepos) - if len(dat) > 0: - dat = [(x,x,'True') for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - -def get_lib_xlsfiles(): - dat = glob.glob('%s/*.xls' % librepos) - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - -def get_lib_htmlfiles(): - dat = glob.glob('%s/*.html' % librepos) - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - -def get_my_xlsfiles(): - dat = glob.glob('%s/*.xls' % myrepos) - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - -def get_my_htmlfiles(): - dat = glob.glob('%s/*.html' % myrepos) - if len(dat) > 0: - dat = [(x,x,False) for x in dat] - else: - dat = [('No ped files - add some to %s' % librepos,'None',True),] - return dat - - diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/plinkbinJZ.py --- a/tools/rgenetics/plinkbinJZ.py +++ /dev/null @@ -1,868 +0,0 @@ -#!/usr/bin/env python2.4 -""" -""" - -import optparse,os,subprocess,gzip,struct,time,commands -from array import array - -#from AIMS import util -#from pga import util as pgautil - -__FILE_ID__ = '$Id: plinkbinJZ.py,v 1.14 2009/07/13 20:16:50 rejpz Exp $' - -VERBOSE = True - -MISSING_ALLELES = set(['N', '0', '.', '-','']) - -AUTOSOMES = set(range(1, 23) + [str(c) for c in range(1, 23)]) - -MAGIC_BYTE1 = '00110110' -MAGIC_BYTE2 = '11011000' -FORMAT_SNP_MAJOR_BYTE = '10000000' -FORMAT_IND_MAJOR_BYTE = '00000000' -MAGIC1 = (0, 3, 1, 2) -MAGIC2 = (3, 1, 2, 0) -FORMAT_SNP_MAJOR = (2, 0, 0, 0) -FORMAT_IND_MAJOR = (0, 0, 0, 0) -HEADER_LENGTH = 3 - -HOM0 = 3 -HOM1 = 0 -MISS = 2 -HET = 1 -HOM0_GENO = (0, 0) -HOM1_GENO = (1, 1) -HET_GENO = (0, 1) -MISS_GENO = (-9, -9) - -GENO_TO_GCODE = { - HOM0_GENO: HOM0, - HET_GENO: HET, - HOM1_GENO: HOM1, - MISS_GENO: MISS, - } - -CHROM_REPLACE = { - 'X': '23', - 'Y': '24', - 'XY': '25', - 'MT': '26', - 'M': '26', -} - -MAP_LINE_EXCEPTION_TEXT = """ -One or more lines in the *.map file has only three fields. -The line was: - -%s - -If you are running rgGRR through EPMP, this is usually a -sign that you are using an old version of the map file. -You can correct the problem by re-running Subject QC. If -you have already tried this, please contact the developers, -or file a bug. -""" - -INT_TO_GCODE = { - 0: array('i', (0, 0, 0, 0)), 1: array('i', (2, 0, 0, 0)), 2: array('i', (1, 0, 0, 0)), 3: array('i', (3, 0, 0, 0)), - 4: array('i', (0, 2, 0, 0)), 5: array('i', (2, 2, 0, 0)), 6: array('i', (1, 2, 0, 0)), 7: array('i', (3, 2, 0, 0)), - 8: array('i', (0, 1, 0, 0)), 9: array('i', (2, 1, 0, 0)), 10: array('i', (1, 1, 0, 0)), 11: array('i', (3, 1, 0, 0)), - 12: array('i', (0, 3, 0, 0)), 13: array('i', (2, 3, 0, 0)), 14: array('i', (1, 3, 0, 0)), 15: array('i', (3, 3, 0, 0)), - 16: array('i', (0, 0, 2, 0)), 17: array('i', (2, 0, 2, 0)), 18: array('i', (1, 0, 2, 0)), 19: array('i', (3, 0, 2, 0)), - 20: array('i', (0, 2, 2, 0)), 21: array('i', (2, 2, 2, 0)), 22: array('i', (1, 2, 2, 0)), 23: array('i', (3, 2, 2, 0)), - 24: array('i', (0, 1, 2, 0)), 25: array('i', (2, 1, 2, 0)), 26: array('i', (1, 1, 2, 0)), 27: array('i', (3, 1, 2, 0)), - 28: array('i', (0, 3, 2, 0)), 29: array('i', (2, 3, 2, 0)), 30: array('i', (1, 3, 2, 0)), 31: array('i', (3, 3, 2, 0)), - 32: array('i', (0, 0, 1, 0)), 33: array('i', (2, 0, 1, 0)), 34: array('i', (1, 0, 1, 0)), 35: array('i', (3, 0, 1, 0)), - 36: array('i', (0, 2, 1, 0)), 37: array('i', (2, 2, 1, 0)), 38: array('i', (1, 2, 1, 0)), 39: array('i', (3, 2, 1, 0)), - 40: array('i', (0, 1, 1, 0)), 41: array('i', (2, 1, 1, 0)), 42: array('i', (1, 1, 1, 0)), 43: array('i', (3, 1, 1, 0)), - 44: array('i', (0, 3, 1, 0)), 45: array('i', (2, 3, 1, 0)), 46: array('i', (1, 3, 1, 0)), 47: array('i', (3, 3, 1, 0)), - 48: array('i', (0, 0, 3, 0)), 49: array('i', (2, 0, 3, 0)), 50: array('i', (1, 0, 3, 0)), 51: array('i', (3, 0, 3, 0)), - 52: array('i', (0, 2, 3, 0)), 53: array('i', (2, 2, 3, 0)), 54: array('i', (1, 2, 3, 0)), 55: array('i', (3, 2, 3, 0)), - 56: array('i', (0, 1, 3, 0)), 57: array('i', (2, 1, 3, 0)), 58: array('i', (1, 1, 3, 0)), 59: array('i', (3, 1, 3, 0)), - 60: array('i', (0, 3, 3, 0)), 61: array('i', (2, 3, 3, 0)), 62: array('i', (1, 3, 3, 0)), 63: array('i', (3, 3, 3, 0)), - 64: array('i', (0, 0, 0, 2)), 65: array('i', (2, 0, 0, 2)), 66: array('i', (1, 0, 0, 2)), 67: array('i', (3, 0, 0, 2)), - 68: array('i', (0, 2, 0, 2)), 69: array('i', (2, 2, 0, 2)), 70: array('i', (1, 2, 0, 2)), 71: array('i', (3, 2, 0, 2)), - 72: array('i', (0, 1, 0, 2)), 73: array('i', (2, 1, 0, 2)), 74: array('i', (1, 1, 0, 2)), 75: array('i', (3, 1, 0, 2)), - 76: array('i', (0, 3, 0, 2)), 77: array('i', (2, 3, 0, 2)), 78: array('i', (1, 3, 0, 2)), 79: array('i', (3, 3, 0, 2)), - 80: array('i', (0, 0, 2, 2)), 81: array('i', (2, 0, 2, 2)), 82: array('i', (1, 0, 2, 2)), 83: array('i', (3, 0, 2, 2)), - 84: array('i', (0, 2, 2, 2)), 85: array('i', (2, 2, 2, 2)), 86: array('i', (1, 2, 2, 2)), 87: array('i', (3, 2, 2, 2)), - 88: array('i', (0, 1, 2, 2)), 89: array('i', (2, 1, 2, 2)), 90: array('i', (1, 1, 2, 2)), 91: array('i', (3, 1, 2, 2)), - 92: array('i', (0, 3, 2, 2)), 93: array('i', (2, 3, 2, 2)), 94: array('i', (1, 3, 2, 2)), 95: array('i', (3, 3, 2, 2)), - 96: array('i', (0, 0, 1, 2)), 97: array('i', (2, 0, 1, 2)), 98: array('i', (1, 0, 1, 2)), 99: array('i', (3, 0, 1, 2)), - 100: array('i', (0, 2, 1, 2)), 101: array('i', (2, 2, 1, 2)), 102: array('i', (1, 2, 1, 2)), 103: array('i', (3, 2, 1, 2)), - 104: array('i', (0, 1, 1, 2)), 105: array('i', (2, 1, 1, 2)), 106: array('i', (1, 1, 1, 2)), 107: array('i', (3, 1, 1, 2)), - 108: array('i', (0, 3, 1, 2)), 109: array('i', (2, 3, 1, 2)), 110: array('i', (1, 3, 1, 2)), 111: array('i', (3, 3, 1, 2)), - 112: array('i', (0, 0, 3, 2)), 113: array('i', (2, 0, 3, 2)), 114: array('i', (1, 0, 3, 2)), 115: array('i', (3, 0, 3, 2)), - 116: array('i', (0, 2, 3, 2)), 117: array('i', (2, 2, 3, 2)), 118: array('i', (1, 2, 3, 2)), 119: array('i', (3, 2, 3, 2)), - 120: array('i', (0, 1, 3, 2)), 121: array('i', (2, 1, 3, 2)), 122: array('i', (1, 1, 3, 2)), 123: array('i', (3, 1, 3, 2)), - 124: array('i', (0, 3, 3, 2)), 125: array('i', (2, 3, 3, 2)), 126: array('i', (1, 3, 3, 2)), 127: array('i', (3, 3, 3, 2)), - 128: array('i', (0, 0, 0, 1)), 129: array('i', (2, 0, 0, 1)), 130: array('i', (1, 0, 0, 1)), 131: array('i', (3, 0, 0, 1)), - 132: array('i', (0, 2, 0, 1)), 133: array('i', (2, 2, 0, 1)), 134: array('i', (1, 2, 0, 1)), 135: array('i', (3, 2, 0, 1)), - 136: array('i', (0, 1, 0, 1)), 137: array('i', (2, 1, 0, 1)), 138: array('i', (1, 1, 0, 1)), 139: array('i', (3, 1, 0, 1)), - 140: array('i', (0, 3, 0, 1)), 141: array('i', (2, 3, 0, 1)), 142: array('i', (1, 3, 0, 1)), 143: array('i', (3, 3, 0, 1)), - 144: array('i', (0, 0, 2, 1)), 145: array('i', (2, 0, 2, 1)), 146: array('i', (1, 0, 2, 1)), 147: array('i', (3, 0, 2, 1)), - 148: array('i', (0, 2, 2, 1)), 149: array('i', (2, 2, 2, 1)), 150: array('i', (1, 2, 2, 1)), 151: array('i', (3, 2, 2, 1)), - 152: array('i', (0, 1, 2, 1)), 153: array('i', (2, 1, 2, 1)), 154: array('i', (1, 1, 2, 1)), 155: array('i', (3, 1, 2, 1)), - 156: array('i', (0, 3, 2, 1)), 157: array('i', (2, 3, 2, 1)), 158: array('i', (1, 3, 2, 1)), 159: array('i', (3, 3, 2, 1)), - 160: array('i', (0, 0, 1, 1)), 161: array('i', (2, 0, 1, 1)), 162: array('i', (1, 0, 1, 1)), 163: array('i', (3, 0, 1, 1)), - 164: array('i', (0, 2, 1, 1)), 165: array('i', (2, 2, 1, 1)), 166: array('i', (1, 2, 1, 1)), 167: array('i', (3, 2, 1, 1)), - 168: array('i', (0, 1, 1, 1)), 169: array('i', (2, 1, 1, 1)), 170: array('i', (1, 1, 1, 1)), 171: array('i', (3, 1, 1, 1)), - 172: array('i', (0, 3, 1, 1)), 173: array('i', (2, 3, 1, 1)), 174: array('i', (1, 3, 1, 1)), 175: array('i', (3, 3, 1, 1)), - 176: array('i', (0, 0, 3, 1)), 177: array('i', (2, 0, 3, 1)), 178: array('i', (1, 0, 3, 1)), 179: array('i', (3, 0, 3, 1)), - 180: array('i', (0, 2, 3, 1)), 181: array('i', (2, 2, 3, 1)), 182: array('i', (1, 2, 3, 1)), 183: array('i', (3, 2, 3, 1)), - 184: array('i', (0, 1, 3, 1)), 185: array('i', (2, 1, 3, 1)), 186: array('i', (1, 1, 3, 1)), 187: array('i', (3, 1, 3, 1)), - 188: array('i', (0, 3, 3, 1)), 189: array('i', (2, 3, 3, 1)), 190: array('i', (1, 3, 3, 1)), 191: array('i', (3, 3, 3, 1)), - 192: array('i', (0, 0, 0, 3)), 193: array('i', (2, 0, 0, 3)), 194: array('i', (1, 0, 0, 3)), 195: array('i', (3, 0, 0, 3)), - 196: array('i', (0, 2, 0, 3)), 197: array('i', (2, 2, 0, 3)), 198: array('i', (1, 2, 0, 3)), 199: array('i', (3, 2, 0, 3)), - 200: array('i', (0, 1, 0, 3)), 201: array('i', (2, 1, 0, 3)), 202: array('i', (1, 1, 0, 3)), 203: array('i', (3, 1, 0, 3)), - 204: array('i', (0, 3, 0, 3)), 205: array('i', (2, 3, 0, 3)), 206: array('i', (1, 3, 0, 3)), 207: array('i', (3, 3, 0, 3)), - 208: array('i', (0, 0, 2, 3)), 209: array('i', (2, 0, 2, 3)), 210: array('i', (1, 0, 2, 3)), 211: array('i', (3, 0, 2, 3)), - 212: array('i', (0, 2, 2, 3)), 213: array('i', (2, 2, 2, 3)), 214: array('i', (1, 2, 2, 3)), 215: array('i', (3, 2, 2, 3)), - 216: array('i', (0, 1, 2, 3)), 217: array('i', (2, 1, 2, 3)), 218: array('i', (1, 1, 2, 3)), 219: array('i', (3, 1, 2, 3)), - 220: array('i', (0, 3, 2, 3)), 221: array('i', (2, 3, 2, 3)), 222: array('i', (1, 3, 2, 3)), 223: array('i', (3, 3, 2, 3)), - 224: array('i', (0, 0, 1, 3)), 225: array('i', (2, 0, 1, 3)), 226: array('i', (1, 0, 1, 3)), 227: array('i', (3, 0, 1, 3)), - 228: array('i', (0, 2, 1, 3)), 229: array('i', (2, 2, 1, 3)), 230: array('i', (1, 2, 1, 3)), 231: array('i', (3, 2, 1, 3)), - 232: array('i', (0, 1, 1, 3)), 233: array('i', (2, 1, 1, 3)), 234: array('i', (1, 1, 1, 3)), 235: array('i', (3, 1, 1, 3)), - 236: array('i', (0, 3, 1, 3)), 237: array('i', (2, 3, 1, 3)), 238: array('i', (1, 3, 1, 3)), 239: array('i', (3, 3, 1, 3)), - 240: array('i', (0, 0, 3, 3)), 241: array('i', (2, 0, 3, 3)), 242: array('i', (1, 0, 3, 3)), 243: array('i', (3, 0, 3, 3)), - 244: array('i', (0, 2, 3, 3)), 245: array('i', (2, 2, 3, 3)), 246: array('i', (1, 2, 3, 3)), 247: array('i', (3, 2, 3, 3)), - 248: array('i', (0, 1, 3, 3)), 249: array('i', (2, 1, 3, 3)), 250: array('i', (1, 1, 3, 3)), 251: array('i', (3, 1, 3, 3)), - 252: array('i', (0, 3, 3, 3)), 253: array('i', (2, 3, 3, 3)), 254: array('i', (1, 3, 3, 3)), 255: array('i', (3, 3, 3, 3)), - } - -GCODE_TO_INT = dict([(tuple(v),k) for (k,v) in INT_TO_GCODE.items()]) - -### Exceptions -class DuplicateMarkerInMapFile(Exception): pass -class MapLineTooShort(Exception): pass -class ThirdAllele(Exception): pass -class PedError(Exception): pass -class BadMagic(Exception): - """ Raised when one of the MAGIC bytes in a bed file does not match - """ - pass -class BedError(Exception): - """ Raised when parsing a bed file runs into problems - """ - pass -class UnknownGenocode(Exception): - """ Raised when we get a 2-bit genotype that is undecipherable (is it possible?) - """ - pass -class UnknownGeno(Exception): pass - -### Utility functions - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -def ceiling(n, k): - ''' Return the least multiple of k which is greater than n - ''' - m = n % k - if m == 0: - return n - else: - return n + k - m - -def nbytes(n): - ''' Return the number of bytes required for n subjects - ''' - return 2*ceiling(n, 4)/8 - -### Primary module functionality -class LPed: - """ The uber-class for processing the Linkage-format *.ped/*.map files - """ - def __init__(self, base): - self.base = base - self._ped = Ped('%s.ped' % (self.base)) - self._map = Map('%s.map' % (self.base)) - - self._markers = {} - self._ordered_markers = [] - self._marker_allele_lookup = {} - self._autosomal_indices = set() - - self._subjects = {} - self._ordered_subjects = [] - - self._genotypes = [] - - def parse(self): - """ - """ - if VERBOSE: print 'plinkbinJZ: Analysis started: %s' % (timenow()) - self._map.parse() - self._markers = self._map._markers - self._ordered_markers = self._map._ordered_markers - self._autosomal_indices = self._map._autosomal_indices - - self._ped.parse(self._ordered_markers) - self._subjects = self._ped._subjects - self._ordered_subjects = self._ped._ordered_subjects - self._genotypes = self._ped._genotypes - self._marker_allele_lookup = self._ped._marker_allele_lookup - - ### Adjust self._markers based on the allele information - ### we got from parsing the ped file - for m, name in enumerate(self._ordered_markers): - a1, a2 = self._marker_allele_lookup[m][HET] - self._markers[name][-2] = a1 - self._markers[name][-1] = a2 - if VERBOSE: print 'plinkbinJZ: Analysis finished: %s' % (timenow()) - - def getSubjectInfo(self, fid, oiid): - """ - """ - return self._subject_info[(fid, oiid)] - - def getSubjectInfoByLine(self, line): - """ - """ - return self._subject_info[self._ordered_subjects[line]] - - def getGenotypesByIndices(self, s, mlist, format): - """ needed for grr if lped - deprecated but.. - """ - mlist = dict(zip(mlist,[True,]*len(mlist))) # hash quicker than 'in' ? - raw_array = array('i', [row[s] for m,row in enumerate(self._genotypes) if mlist.get(m,None)]) - if format == 'raw': - return raw_array - elif format == 'ref': - result = array('i', [0]*len(mlist)) - for m, gcode in enumerate(raw_array): - if gcode == HOM0: - nref = 3 - elif gcode == HET: - nref = 2 - elif gcode == HOM1: - nref = 1 - else: - nref = 0 - result[m] = nref - return result - else: - result = [] - for m, gcode in enumerate(raw_array): - result.append(self._marker_allele_lookup[m][gcode]) - return result - - def writebed(self, base): - """ - """ - dst_name = '%s.fam' % (base) - print 'Writing pedigree information to [ %s ]' % (dst_name) - dst = open(dst_name, 'w') - for skey in self._ordered_subjects: - (fid, iid, did, mid, sex, phe, sid, d_sid, m_sid) = self._subjects[skey] - dst.write('%s %s %s %s %s %s\n' % (fid, iid, did, mid, sex, phe)) - dst.close() - - dst_name = '%s.bim' % (base) - print 'Writing map (extended format) information to [ %s ]' % (dst_name) - dst = open(dst_name, 'w') - for m, marker in enumerate(self._ordered_markers): - chrom, name, genpos, abspos, a1, a2 = self._markers[marker] - dst.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (chrom, name, genpos, abspos, a1, a2)) - dst.close() - - bed_name = '%s.bed' % (base) - print 'Writing genotype bitfile to [ %s ]' % (bed_name) - print 'Using (default) SNP-major mode' - bed = open(bed_name, 'w') - - ### Write the 3 header bytes - bed.write(struct.pack('B', int(''.join(reversed(MAGIC_BYTE1)), 2))) - bed.write(struct.pack('B', int(''.join(reversed(MAGIC_BYTE2)), 2))) - bed.write(struct.pack('B', int(''.join(reversed(FORMAT_SNP_MAJOR_BYTE)), 2))) - - ### Calculate how many "pad bits" we should add after the last subject - nsubjects = len(self._ordered_subjects) - nmarkers = len(self._ordered_markers) - total_bytes = nbytes(nsubjects) - nbits = nsubjects * 2 - pad_nibbles = ((total_bytes * 8) - nbits)/2 - pad = array('i', [0]*pad_nibbles) - - ### And now write genotypes to the file - for m in xrange(nmarkers): - geno = self._genotypes[m] - geno.extend(pad) - bytes = len(geno)/4 - for b in range(bytes): - idx = b*4 - gcode = tuple(geno[idx:idx+4]) - try: - byte = struct.pack('B', GCODE_TO_INT[gcode]) - except KeyError: - print m, b, gcode - raise - bed.write(byte) - bed.close() - - def autosomal_indices(self): - """ Return the indices of markers in this ped/map that are autosomal. - This is used by rgGRR so that it can select a random set of markers - from the autosomes (sex chroms screw up the plot) - """ - return self._autosomal_indices - -class Ped: - def __init__(self, path): - self.path = path - self._subjects = {} - self._ordered_subjects = [] - self._genotypes = [] - self._marker_allele_lookup = {} - - def lineCount(self,infile): - """ count the number of lines in a file - efficiently using wget - """ - return int(commands.getoutput('wc -l %s' % (infile)).split()[0]) - - - def parse(self, markers): - """ Parse a given file -- this needs to be memory-efficient so that large - files can be parsed (~1 million markers on ~5000 subjects?). It - should also be fast, if possible. - """ - - ### Find out how many lines are in the file so we can ... - nsubjects = self.lineCount(self.path) - ### ... Pre-allocate the genotype arrays - nmarkers = len(markers) - _marker_alleles = [['0', '0'] for _ in xrange(nmarkers)] - self._genotypes = [array('i', [-1]*nsubjects) for _ in xrange(nmarkers)] - - if self.path.endswith('.gz'): - pfile = gzip.open(self.path, 'r') - else: - pfile = open(self.path, 'r') - - for s, line in enumerate(pfile): - line = line.strip() - if not line: - continue - - fid, iid, did, mid, sex, phe, genos = line.split(None, 6) - sid = iid.split('.')[0] - d_sid = did.split('.')[0] - m_sid = mid.split('.')[0] - - skey = (fid, iid) - self._subjects[skey] = (fid, iid, did, mid, sex, phe, sid, d_sid, m_sid) - self._ordered_subjects.append(skey) - - genotypes = genos.split() - - for m, marker in enumerate(markers): - idx = m*2 - a1, a2 = genotypes[idx:idx+2] # Alleles for subject s, marker m - s1, s2 = seen = _marker_alleles[m] # Alleles seen for marker m - - ### FIXME: I think this can still be faster, and simpler to read - # Two pieces of logic intertwined here: first, we need to code - # this genotype as HOM0, HOM1, HET or MISS. Second, we need to - # keep an ongoing record of the genotypes seen for this marker - if a1 == a2: - if a1 in MISSING_ALLELES: - geno = MISS_GENO - else: - if s1 == '0': - seen[0] = a1 - elif s1 == a1 or s2 == a2: - pass - elif s2 == '0': - seen[1] = a1 - else: - raise ThirdAllele('a1=a2=%s, seen=%s?' % (a1, str(seen))) - - if a1 == seen[0]: - geno = HOM0_GENO - elif a1 == seen[1]: - geno = HOM1_GENO - else: - raise PedError('Cannot assign geno for a1=a2=%s from seen=%s' % (a1, str(seen))) - elif a1 in MISSING_ALLELES or a2 in MISSING_ALLELES: - geno = MISS_GENO - else: - geno = HET_GENO - if s1 == '0': - seen[0] = a1 - seen[1] = a2 - elif s2 == '0': - if s1 == a1: - seen[1] = a2 - elif s1 == a2: - seen[1] = a1 - else: - raise ThirdAllele('a1=%s, a2=%s, seen=%s?' % (a1, a2, str(seen))) - else: - if sorted(seen) != sorted((a1, a2)): - raise ThirdAllele('a1=%s, a2=%s, seen=%s?' % (a1, a2, str(seen))) - - gcode = GENO_TO_GCODE.get(geno, None) - if gcode is None: - raise UnknownGeno(str(geno)) - self._genotypes[m][s] = gcode - - # Build the _marker_allele_lookup table - for m, alleles in enumerate(_marker_alleles): - if len(alleles) == 2: - a1, a2 = alleles - elif len(alleles) == 1: - a1 = alleles[0] - a2 = '0' - else: - print 'All alleles blank for %s: %s' % (m, str(alleles)) - raise - - self._marker_allele_lookup[m] = { - HOM0: (a2, a2), - HOM1: (a1, a1), - HET : (a1, a2), - MISS: ('0','0'), - } - - if VERBOSE: print '%s(%s) individuals read from [ %s ]' % (len(self._subjects), nsubjects, self.path) - -class Map: - def __init__(self, path=None): - self.path = path - self._markers = {} - self._ordered_markers = [] - self._autosomal_indices = set() - - def __len__(self): - return len(self._markers) - - def parse(self): - """ Parse a Linkage-format map file - """ - if self.path.endswith('.gz'): - fh = gzip.open(self.path, 'r') - else: - fh = open(self.path, 'r') - - for i, line in enumerate(fh): - line = line.strip() - if not line: - continue - - fields = line.split() - if len(fields) < 4: - raise MapLineTooShort(MAP_LINE_EXCEPTION_TEXT % (str(line), len(fields))) - else: - chrom, name, genpos, abspos = fields - if name in self._markers: - raise DuplicateMarkerInMapFile('Marker %s was found twice in map file %s' % (name, self.path)) - abspos = int(abspos) - if abspos < 0: - continue - if chrom in AUTOSOMES: - self._autosomal_indices.add(i) - chrom = CHROM_REPLACE.get(chrom, chrom) - self._markers[name] = [chrom, name, genpos, abspos, None, None] - self._ordered_markers.append(name) - fh.close() - if VERBOSE: print '%s (of %s) markers to be included from [ %s ]' % (len(self._ordered_markers), i, self.path) - -class BPed: - """ The uber-class for processing Plink's Binary Ped file format *.bed/*.bim/*.fam - """ - def __init__(self, base): - self.base = base - self._bed = Bed('%s.bed' % (self.base)) - self._bim = Bim('%s.bim' % (self.base)) - self._fam = Fam('%s.fam' % (self.base)) - - self._markers = {} - self._ordered_markers = [] - self._marker_allele_lookup = {} - self._autosomal_indices = set() - - self._subjects = {} - self._ordered_subjects = [] - - self._genotypes = [] - - def parse(self, quick=False): - """ - """ - self._quick = quick - - self._bim.parse() - self._markers = self._bim._markers - self._ordered_markers = self._bim._ordered_markers - self._marker_allele_lookup = self._bim._marker_allele_lookup - self._autosomal_indices = self._bim._autosomal_indices - - self._fam.parse() - self._subjects = self._fam._subjects - self._ordered_subjects = self._fam._ordered_subjects - - self._bed.parse(self._ordered_subjects, self._ordered_markers, quick=quick) - self._bedf = self._bed._fh - self._genotypes = self._bed._genotypes - self.nsubjects = len(self._ordered_subjects) - self.nmarkers = len(self._ordered_markers) - self._bytes_per_marker = nbytes(self.nsubjects) - - def writeped(self, path=None): - """ - """ - path = self.path = path or self.path - - map_name = self.path.replace('.bed', '.map') - print 'Writing map file [ %s ]' % (map_name) - dst = open(map_name, 'w') - for m in self._ordered_markers: - chrom, snp, genpos, abspos, a1, a2 = self._markers[m] - dst.write('%s\t%s\t%s\t%s\n' % (chrom, snp, genpos, abspos)) - dst.close() - - ped_name = self.path.replace('.bed', '.ped') - print 'Writing ped file [ %s ]' % (ped_name) - ped = open(ped_name, 'w') - firstyikes = False - for s, skey in enumerate(self._ordered_subjects): - idx = s*2 - (fid, iid, did, mid, sex, phe, oiid, odid, omid) = self._subjects[skey] - ped.write('%s %s %s %s %s %s' % (fid, iid, odid, omid, sex, phe)) - genotypes_for_subject = self.getGenotypesForSubject(s) - for m, snp in enumerate(self._ordered_markers): - #a1, a2 = self.getGenotypeByIndices(s, m) - a1,a2 = genotypes_for_subject[m] - ped.write(' %s %s' % (a1, a2)) - ped.write('\n') - ped.close() - - def getGenotype(self, subject, marker): - """ Retrieve a genotype for a particular subject/marker pair - """ - m = self._ordered_markers.index(marker) - s = self._ordered_subjects.index(subject) - return self.getGenotypeByIndices(s, m) - - def getGenotypesForSubject(self, s, raw=False): - """ Returns list of genotypes for all m markers - for subject s. If raw==True, then an array - of raw integer gcodes is returned instead - """ - if self._quick: - nmarkers = len(self._markers) - raw_array = array('i', [0]*nmarkers) - seek_nibble = s % 4 - for m in xrange(nmarkers): - seek_byte = m * self._bytes_per_marker + s/4 + HEADER_LENGTH - self._bedf.seek(seek_byte) - geno = struct.unpack('B', self._bedf.read(1))[0] - quartet = INT_TO_GCODE[geno] - gcode = quartet[seek_nibble] - raw_array[m] = gcode - else: - raw_array = array('i', [row[s] for row in self._genotypes]) - - if raw: - return raw_array - else: - result = [] - for m, gcode in enumerate(raw_array): - result.append(self._marker_allele_lookup[m][gcode]) - return result - - def getGenotypeByIndices(self, s, m): - """ - """ - if self._quick: - # Determine which byte we need to seek to, and - # which nibble within the byte we need - seek_byte = m * self._bytes_per_marker + s/4 + HEADER_LENGTH - seek_nibble = s % 4 - self._bedf.seek(seek_byte) - geno = struct.unpack('B', self._bedf.read(1))[0] - quartet = INT_TO_GCODE[geno] - gcode = quartet[seek_nibble] - else: - # Otherwise, just grab the genotypes from the - # list of arrays - genos_for_marker = self._genotypes[m] - gcode = genos_for_marker[s] - - return self._marker_allele_lookup[m][gcode] - - def getGenotypesByIndices(self, s, mlist, format): - """ - """ - if self._quick: - raw_array = array('i', [0]*len(mlist)) - seek_nibble = s % 4 - for i,m in enumerate(mlist): - seek_byte = m * self._bytes_per_marker + s/4 + HEADER_LENGTH - self._bedf.seek(seek_byte) - geno = struct.unpack('B', self._bedf.read(1))[0] - quartet = INT_TO_GCODE[geno] - gcode = quartet[seek_nibble] - raw_array[i] = gcode - mlist = set(mlist) - else: - mlist = set(mlist) - raw_array = array('i', [row[s] for m,row in enumerate(self._genotypes) if m in mlist]) - - if format == 'raw': - return raw_array - elif format == 'ref': - result = array('i', [0]*len(mlist)) - for m, gcode in enumerate(raw_array): - if gcode == HOM0: - nref = 3 - elif gcode == HET: - nref = 2 - elif gcode == HOM1: - nref = 1 - else: - nref = 0 - result[m] = nref - return result - else: - result = [] - for m, gcode in enumerate(raw_array): - result.append(self._marker_allele_lookup[m][gcode]) - return result - - def getSubject(self, s): - """ - """ - skey = self._ordered_subjects[s] - return self._subjects[skey] - - def autosomal_indices(self): - """ Return the indices of markers in this ped/map that are autosomal. - This is used by rgGRR so that it can select a random set of markers - from the autosomes (sex chroms screw up the plot) - """ - return self._autosomal_indices - -class Bed: - - def __init__(self, path): - self.path = path - self._genotypes = [] - self._fh = None - - def parse(self, subjects, markers, quick=False): - """ Parse the bed file, indicated either by the path parameter, - or as the self.path indicated in __init__. If quick is - True, then just parse the bim and fam, then genotypes will - be looked up dynamically by indices - """ - self._quick = quick - - ordered_markers = markers - ordered_subjects = subjects - nsubjects = len(ordered_subjects) - nmarkers = len(ordered_markers) - - bed = open(self.path, 'rb') - self._fh = bed - - byte1 = bed.read(1) - byte2 = bed.read(1) - byte3 = bed.read(1) - format_flag = struct.unpack('B', byte3)[0] - - h1 = tuple(INT_TO_GCODE[struct.unpack('B', byte1)[0]]) - h2 = tuple(INT_TO_GCODE[struct.unpack('B', byte2)[0]]) - h3 = tuple(INT_TO_GCODE[format_flag]) - - if h1 != MAGIC1 or h2 != MAGIC2: - raise BadMagic('One or both MAGIC bytes is wrong: %s==%s or %s==%s' % (h1, MAGIC1, h2, MAGIC2)) - if format_flag: - print 'Detected that binary PED file is v1.00 SNP-major mode (%s, "%s")\n' % (format_flag, h3) - else: - raise 'BAD_FORMAT_FLAG? (%s, "%s")\n' % (format_flag, h3) - - print 'Parsing binary ped file for %s markers and %s subjects' % (nmarkers, nsubjects) - - ### If quick mode was specified, we're done ... - self._quick = quick - if quick: - return - - ### ... Otherwise, parse genotypes into an array, and append that - ### array to self._genotypes - ngcodes = ceiling(nsubjects, 4) - bytes_per_marker = nbytes(nsubjects) - for m in xrange(nmarkers): - genotype_array = array('i', [-1]*(ngcodes)) - for byte in xrange(bytes_per_marker): - intval = struct.unpack('B', bed.read(1))[0] - idx = byte*4 - genotype_array[idx:idx+4] = INT_TO_GCODE[intval] - self._genotypes.append(genotype_array) - -class Bim: - def __init__(self, path): - """ - """ - self.path = path - self._markers = {} - self._ordered_markers = [] - self._marker_allele_lookup = {} - self._autosomal_indices = set() - - def parse(self): - """ - """ - print 'Reading map (extended format) from [ %s ]' % (self.path) - bim = open(self.path, 'r') - for m, line in enumerate(bim): - chrom, snp, gpos, apos, a1, a2 = line.strip().split() - self._markers[snp] = (chrom, snp, gpos, apos, a1, a2) - self._marker_allele_lookup[m] = { - HOM0: (a2, a2), - HOM1: (a1, a1), - HET : (a1, a2), - MISS: ('0','0'), - } - self._ordered_markers.append(snp) - if chrom in AUTOSOMES: - self._autosomal_indices.add(m) - bim.close() - print '%s markers to be included from [ %s ]' % (m+1, self.path) - -class Fam: - def __init__(self, path): - """ - """ - self.path = path - self._subjects = {} - self._ordered_subjects = [] - - def parse(self): - """ - """ - print 'Reading pedigree information from [ %s ]' % (self.path) - fam = open(self.path, 'r') - for s, line in enumerate(fam): - fid, iid, did, mid, sex, phe = line.strip().split() - sid = iid.split('.')[0] - d_sid = did.split('.')[0] - m_sid = mid.split('.')[0] - skey = (fid, iid) - self._ordered_subjects.append(skey) - self._subjects[skey] = (fid, iid, did, mid, sex, phe, sid, d_sid, m_sid) - fam.close() - print '%s individuals read from [ %s ]' % (s+1, self.path) - -### Command-line functionality and testing -def test(arg): - ''' - ''' - - import time - - if arg == 'CAMP_AFFY.ped': - print 'Testing bed.parse(quick=True)' - s = time.time() - bed = Bed(arg.replace('.ped', '.bed')) - bed.parse(quick=True) - print bed.getGenotype(('400118', '10300283'), 'rs2000467') - print bed.getGenotype(('400118', '10101384'), 'rs2294019') - print bed.getGenotype(('400121', '10101149'), 'rs2294019') - print bed.getGenotype(('400123', '10200290'), 'rs2294019') - assert bed.getGenotype(('400118', '10101384'), 'rs2294019') == ('4','4') - e = time.time() - print 'e-s = %s\n' % (e-s) - - print 'Testing bed.parse' - s = time.time() - bed = BPed(arg) - bed.parse(quick=False) - e = time.time() - print 'e-s = %s\n' % (e-s) - - print 'Testing bed.writeped' - s = time.time() - outname = '%s_BEDTEST' % (arg) - bed.writeped(outname) - e = time.time() - print 'e-s = %s\n' % (e-s) - del(bed) - - print 'Testing ped.parse' - s = time.time() - ped = LPed(arg) - ped.parse() - e = time.time() - print 'e-s = %s\n' % (e-s) - - print 'Testing ped.writebed' - s = time.time() - outname = '%s_PEDTEST' % (arg) - ped.writebed(outname) - e = time.time() - print 'e-s = %s\n' % (e-s) - del(ped) - -def profile_bed(arg): - """ - """ - bed = BPed(arg) - bed.parse(quick=False) - outname = '%s_BEDPROFILE' % (arg) - bed.writeped(outname) - -def profile_ped(arg): - """ - """ - ped = LPed(arg) - ped.parse() - outname = '%s_PEDPROFILE' % (arg) - ped.writebed(outname) - -if __name__ == '__main__': - """ Run as a command-line, this script should get one or more arguments, - each one a ped file to be parsed with the PedParser (unit tests?) - """ - op = optparse.OptionParser() - op.add_option('--profile-bed', action='store_true', default=False) - op.add_option('--profile-ped', action='store_true', default=False) - opts, args = op.parse_args() - - if opts.profile_bed: - import profile - import pstats - profile.run('profile_bed(args[0])', 'fooprof') - p = pstats.Stats('fooprof') - p.sort_stats('cumulative').print_stats(10) - elif opts.profile_ped: - import profile - import pstats - profile.run('profile_ped(args[0])', 'fooprof') - p = pstats.Stats('fooprof') - p.sort_stats('cumulative').print_stats(10) - else: - for arg in args: - test(arg) - - ### Code used to generate the INT_TO_GCODE dictionary - #print '{\n ', - #for i in range(256): - # b = INT2BIN[i] - # ints = [] - # s = str(i).rjust(3) - # #print b - # for j in range(4): - # idx = j*2 - # #print i, j, idx, b[idx:idx+2], int(b[idx:idx+2], 2) - # ints.append(int(b[idx:idx+2], 2)) - # print '%s: array(\'i\', %s),' % (s,tuple(ints)), - # if i > 0 and (i+1) % 4 == 0: - # print '\n ', - #print '}' - - diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/rgCaCo.py --- a/tools/rgenetics/rgCaCo.py +++ /dev/null @@ -1,271 +0,0 @@ -#!/usr/local/bin/python -# hack to run and process a plink case control association -# expects args as -# bfilepath outname jobname outformat (wig,xls) -# ross lazarus -# for wig files, we need annotation so look for map file or complain -""" -Parameters for wiggle track definition lines -All options are placed in a single line separated by spaces: - - track type=wiggle_0 name=track_label description=center_label \ - visibility=display_mode color=r,g,b altColor=r,g,b \ - priority=priority autoScale=on|off \ - gridDefault=on|off maxHeightPixels=max:default:min \ - graphType=bar|points viewLimits=lower:upper \ - yLineMark=real-value yLineOnOff=on|off \ - windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16 -""" - -import sys,math,shutil,subprocess,os,time,tempfile,string -from os.path import abspath -from rgutils import timenow, plinke -imagedir = '/static/rg' # if needed for images -myversion = 'V000.1 April 2007' -verbose = False - -def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000): - """ - score must be scaled to 0-1000 - - Want to make some wig tracks from each analysis - Best n -log10(p). Make top hit the window. - we use our tab output which has - rs chrom offset ADD_stat ADD_p ADD_log10p - rs3094315 1 792429 1.151 0.2528 0.597223 - - """ - - def is_number(s): - try: - float(s) - return True - except ValueError: - return False - header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description) - column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] - halfwidth=100 - resfpath = os.path.join(twd,resf) - resf = open(resfpath,'r') - resfl = resf.readlines() # dumb but convenient for millions of rows - resfl = [x.split() for x in resfl] - headl = resfl[0] - resfl = resfl[1:] - headl = [x.strip().upper() for x in headl] - headIndex = dict(zip(headl,range(0,len(headl)))) - whatwewant = ['CHR','RS','OFFSET','LOG10ARMITAGEP'] - wewant = [headIndex.get(x,None) for x in whatwewant] - if None in wewant: # missing something - logf.write('### Error missing a required header from %s in makeGFF - headIndex=%s\n' % (whatwewant,headIndex)) - return - ppos = wewant[3] # last in list - resfl = [x for x in resfl if x[ppos] > '' and x[ppos] <> 'NA'] - resfl = [(float(x[ppos]),x) for x in resfl] # decorate - resfl.sort() - resfl.reverse() # using -log10 so larger is better - pvals = [x[0] for x in resfl] # need to scale - resfl = [x[1] for x in resfl] # drop decoration - resfl = resfl[:topn] # truncate - maxp = max(pvals) # need to scale - minp = min(pvals) - prange = abs(maxp-minp) + 0.5 # fudge - scalefact = 1000.0/prange - logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) - for i,row in enumerate(resfl): - row[ppos] = '%d' % (int(scalefact*pvals[i])) - resfl[i] = row # replace - outf = file(outfname,'w') - outf.write(header) - outres = [] # need to resort into chrom offset order - for i,lrow in enumerate(resfl): - chrom,snp,offset,p, = [lrow[x] for x in wewant] - gff = ('chr%s' % chrom,'rgCaCo','variation','%d' % (int(offset)-halfwidth), - '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i])) - outres.append(gff) - outres = [(x[0],int(x[3]),x) for x in outres] # decorate - outres.sort() # into chrom offset - outres=[x[2] for x in outres] # undecorate - outres = ['\t'.join(x) for x in outres] - outf.write('\n'.join(outres)) - outf.write('\n') - outf.close() - - -def plink_assocToGG(plinkout="hm",tag='test'): - """ plink --assoc output looks like this - # CHR SNP A1 F_A F_U A2 CHISQ P OR - # 1 rs3094315 G 0.6685 0.1364 A 104.1 1.929e-24 12.77 - # write as a genegraph input file - """ - inf = file('%s.assoc' % plinkout,'r') - outf = file('%sassoc.xls' % plinkout,'w') - res = ['rs\tlog10p%s\tFakeInvOR%s\tRealOR%s' % (tag,tag,tag),] # output header for ucsc genome graphs - head = inf.next() - for l in inf: - ll = l.split() - if len(ll) >= 8: - p = float(ll[7]) - if p <> 'NA': # eesh - logp = '%9.9f' % -math.log10(p) - else: - logp = 'NA' - try: - orat = ll[8] - except: - orat = 'NA' - orat2 = orat - # invert large negative odds ratios - if float(orat) < 1 and float(orat) > 0.0: - orat2 = '%9.9f' % (1.0/float(orat)) - outl = [ll[1],logp, orat2, orat] - res.append('\t'.join(outl)) - outf.write('\n'.join(res)) - outf.write('\n') - outf.close() - inf.close() - -def xformModel(infname='',resf='',outfname='', - name='foo',mapf='/usr/local/galaxy/data/rg/ped/x.bim',flog=None): - """munge a plink .model file into either a ucsc track or an xls file - rerla@meme ~/plink]$ head hmYRI_CEU.model - CHR SNP TEST AFF UNAFF CHISQ DF P - 1 rs3094315 GENO 41/37/11 0/24/64 NA NA NA - 1 rs3094315 TREND 119/59 24/152 81.05 1 2.201e-19 - 1 rs3094315 ALLELIC 119/59 24/152 104.1 1 1.929e-24 - 1 rs3094315 DOM 78/11 24/64 NA NA NA - - bim file has -[rerla@beast pbed]$ head plink_wgas1_example.bim -1 rs3094315 0.792429 792429 G A -1 rs6672353 0.817376 817376 A G - """ - if verbose: - print 'Rgenetics rgCaCo.xformModel got resf=%s, outfname=%s' % (resf,outfname) - res = [] - rsdict = {} - map = file(mapf,'r') - for l in map: # plink map - ll = l.strip().split() - if len(ll) >= 3: - rs=ll[1].strip() - chrom = ll[0] - if chrom.lower() == 'x': - chrom='23' - elif chrom.lower() == 'y': - chrom = 24 - elif chrom.lower() == 'mito': - chrom = 25 - offset = ll[3] - rsdict[rs] = (chrom,offset) - res.append('rs\tChr\tOffset\tGenop\tlog10Genop\tArmitagep\tlog10Armitagep\tAllelep\tlog10Allelep\tDomp\tlog10Domp') - f = open(resf,'r') - headl = f.readline() - if headl.find('\t') <> -1: - headl = headl.split('\t') - delim = '\t' - else: - headl = headl.split() - delim = None - whatwewant = ['CHR','SNP','TEST','AFF','UNAFF','CHISQ','P'] - wewant = [headl.index(x) for x in whatwewant] - llen = len(headl) - lnum = anum = 0 - lastsnp = None # so we know when to write out a gg line - outl = {} - f.seek(0) - for lnum,l in enumerate(f): - if lnum == 0: - continue - ll = l.split() - if delim: - ll = l.split(delim) - if len(ll) >= llen: # valid line - chr,snp,test,naff,nuaff,chi,p = [ll[x] for x in wewant] - snp = snp.strip() - chrom,offset = rsdict.get(snp,(None,None)) - anum += 1 - fp = 1.0 # if NA - lp = 0.0 - try: - fp = float(p) - if fp > 0: - lp = -math.log10(fp) - else: - fp = 9e-100 - flog.write('### WARNING - Plink calculated %s for %s p value!!! 9e-100 substituted!\n' % (p,test)) - flog.write('### offending line #%d in %s = %s' % (lnum,l)) - except: - pass - if snp <> lastsnp: - if len(outl.keys()) > 3: - sl = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')] - res.append('\t'.join(sl)) # last snp line - outl = {'snp':snp,'chrom':chrom,'offset':offset} # first 3 cols for gg line - lastsnp = snp # reset for next marker - #if p == 'NA': - # p = 1.0 - # let's pass downstream for handling R is fine? - outl[test] = '%s\t%f' % (p,lp) - if len(outl.keys()) > 3: - l = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')] - res.append('\t'.join(l)) # last snp line - f = file(outfname,'w') - res.append('') - f.write('\n'.join(res)) - f.close() - - - - -if __name__ == "__main__": - """ - # called as - <command interpreter="python"> - rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" - '$out_file1' '$logf' '$logf.files_path' '$gffout' - </command></command> - """ - if len(sys.argv) < 7: - s = 'rgCaCo.py needs 6 params - got %s \n' % (sys.argv) - print >> sys.stdout, s - sys.exit(0) - bfname = sys.argv[1] - name = sys.argv[2] - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - name = name.translate(trantab) - outfname = sys.argv[3] - logf = sys.argv[4] - logoutdir = sys.argv[5] - gffout = sys.argv[6] - topn = 1000 - try: - os.makedirs(logoutdir) - except: - pass - map_file = None - me = sys.argv[0] - amapf = '%s.bim' % bfname # to decode map in xformModel - flog = file(logf,'w') - logme = [] - cdir = os.getcwd() - s = 'Rgenetics %s http://rgenetics.org Galaxy Tools, rgCaCo.py started %s\n' % (myversion,timenow()) - print >> sys.stdout, s # so will appear as blurb for file - logme.append(s) - if verbose: - s = 'rgCaCo.py: bfname=%s, logf=%s, argv = %s\n' % (bfname, logf, sys.argv) - print >> sys.stdout, s # so will appear as blurb for file - logme.append(s) - twd = tempfile.mkdtemp(suffix='rgCaCo') # make sure plink doesn't spew log file into the root! - tname = os.path.join(twd,name) - vcl = [plinke,'--noweb','--bfile',bfname,'--out',name,'--model'] - p=subprocess.Popen(' '.join(vcl),shell=True,stdout=flog,cwd=twd) - retval = p.wait() - resf = '%s.model' % tname # plink output is here we hope - xformModel(bfname,resf,outfname,name,amapf,flog) # leaves the desired summary file - makeGFF(resf=outfname,outfname=gffout,logf=flog,twd=twd,name='rgCaCo_TopTable',description=name,topn=topn) - flog.write('\n'.join(logme)) - flog.close() # close the log used - #shutil.copytree(twd,logoutdir) - shutil.rmtree(twd) # clean up - diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ /dev/null @@ -1,104 +0,0 @@ -<tool id="rgCaCo1" name="Case Control:"> - <requirements><requirement type="package">plink</requirement></requirements> - <description>for unrelated subjects</description> - <command interpreter="python"> - rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' - </command> - <inputs> - <param name="i" type="data" label="RGenetics genotype data from your current history" - format="pbed" /> - <param name='title' type='text' size="132" value='CaseControl' label="Title for this job"/> - - </inputs> - - <outputs> - <data format="tabular" name="out_file1" label="${title}_rgCaCo.xls" /> - <data format="txt" name="logf" label="${title}_rgCaCo.log"/> - <data format="gff" name="gffout" label="${title}_rgCaCoTop.gff" /> - </outputs> -<tests> - <test> - <param name='i' value='tinywga' ftype='pbed' > - <metadata name='base_name' value='tinywga' /> - <composite_data value='tinywga.bim' /> - <composite_data value='tinywga.bed' /> - <composite_data value='tinywga.fam' /> - <edit_attributes type='name' value='tinywga' /> - </param> - <param name='title' value='rgCaCotest1' /> - <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /> - <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' /> - <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' /> - </test> -</tests> -<help> - -.. class:: infomark - -**Syntax** - -- **Genotype file** is the input case control data chosen from available library Plink binary files -- **Map file** is the linkage format .map file corresponding to the genotypes in the Genotype file -- **Type of test** is the kind of test statistic to report such as Armitage trend test or genotype test -- **Format** determines how your data will be returned to your Galaxy workspace - ------ - -**Summary** - -This tool will perform some standard statistical tests comparing subjects designated as -affected (cases) and unaffected subjects (controls). To avoid bias, it is important that -controls who had been affected would have been eligible for sampling as cases. This may seem -odd, but it requires that the cases and controls are drawn from the same sampling frame. - -The armitage trend test is robust to departure from HWE and so very attractive - after all, a real disease -mutation may well result in distorted HWE at least in cases. All the others are susceptible to -bias in the presence of HWE departures. - -All of these tests are exquisitely sensitive to non-differential population stratification in cases -compared to controls and this must be tested before believing any results here. Use the PCA method for -100k markers or more. - -If you don't see the genotype data set you want here, it can be imported using one of the methods available from -the Galaxy Get Data tool page. - -Output format can be UCSC .bed if you want to see your -results as a fully fledged UCSC track. A map file containing the chromosome and offset for each marker is required for -writing this kind of output. -Alternatively you can use .gg for the UCSC Genome Graphs tool which has all of the advantages -of the the .bed track, plus a neat, visual front end that displays a lot of useful clues. -Either of these are a very useful way of quickly getting a look -at your data in full genomic context. - -Finally, if you can't live without -spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited -one with a header. Fortunately excel is dumb enough to open these without much protest. - - ------ - -.. class:: infomark - -**Attribution** - -This Galaxy tool relies on Plink (see Plinksrc_) to test Casae Control association models. - -So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see -DOC_ - -Tool and Galaxy datatypes originally designed and written for the Rgenetics -series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus(a)gmail.com) - -Copyright Ross Lazarus March 2007 -This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL. - -I'm no lawyer, but it looks like you got GPL if you use this software. Good luck. - -.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html - -.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#cc - -</help> -</tool> diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/rgClean.py --- a/tools/rgenetics/rgClean.py +++ /dev/null @@ -1,160 +0,0 @@ -""" -# galaxy tool xml files can define a galaxy supplied output filename -# that must be passed to the tool and used to return output -# here, the plink log file is copied to that file and removed -# took a while to figure this out! -# use exec_before_job to give files sensible names -# -# ross april 14 2007 -# plink cleanup script -# ross lazarus March 2007 for camp illumina whole genome data -# note problems with multiple commands being ignored - eg --freq --missing --mendel -# only the first seems to get done... -# -##Summary statistics versus inclusion criteria -## -##Feature As summary statistic As inclusion criteria -##Missingness per individual --missing --mind N -##Missingness per marker --missing --geno N -##Allele frequency --freq --maf N -##Hardy-Weinberg equilibrium --hardy --hwe N -##Mendel error rates --mendel --me N M -# -# call as plinkClean.py $i $o $mind $geno $hwe $maf $mef $mei $outfile -# note plinkClean_code.py does some renaming before the job starts - - - <command interpreter="python2.4"> - rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' '$geno' '$hwe' '$maf' - '$mef' '$mei' '$out_file1' '$out_file1.files_path' '$userId' - - -""" -import sys,shutil,os,subprocess, glob, string, tempfile, time -from rgutils import galhtmlprefix, timenow, plinke -prog = os.path.split(sys.argv[0])[-1] -myversion = 'January 4 2010' -verbose=False - - -def fixoutaff(outpath='',newaff='1'): - """ quick way to create test data sets - set all aff to 1 or 2 for - some hapmap data and then merge - [rerla@beast galaxy]$ head tool-data/rg/library/pbed/affyHM_CEU.fam - 1341 14 0 0 2 1 - 1341 2 13 14 2 1 - 1341 13 0 0 1 1 - 1340 9 0 0 1 1 - 1340 10 0 0 2 1 - """ - nchanged = 0 - fam = '%s.fam' % outpath - famf = open(fam,'r') - fl = famf.readlines() - famf.close() - for i,row in enumerate(fl): - lrow = row.split() - if lrow[-1] <> newaff: - lrow[-1] = newaff - fl[i] = ' '.join(lrow) - fl[i] += '\n' - nchanged += 1 - fo = open(fam,'w') - fo.write(''.join(fl)) - fo.close() - return nchanged - - - -def clean(): - """ - """ - if len(sys.argv) < 16: - print >> sys.stdout, '## %s expected 12 params in sys.argv, got %d - %s' % (prog,len(sys.argv),sys.argv) - print >> sys.stdout, """this script will filter a linkage format ped - and map file containing genotypes. It takes 14 parameters - the plink --f parameter and" - a new filename root for the output clean data followed by the mind,geno,hwe,maf, mef and mei" - documented in the plink docs plus the file to be returned to Galaxy - called as: - <command interpreter="python"> - rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' - '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path' - '$relfilter' '$afffilter' '$sexfilter' '$fixaff' - </command> - - """ - sys.exit(1) - plog = [] - inpath = sys.argv[1] - inbase = sys.argv[2] - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - title = sys.argv[3].translate(trantab) - mind = sys.argv[4] - geno = sys.argv[5] - hwe = sys.argv[6] - maf = sys.argv[7] - me1 = sys.argv[8] - me2 = sys.argv[9] - outfname = sys.argv[10] - outfpath = sys.argv[11] - relf = sys.argv[12] - afff = sys.argv[13] - sexf = sys.argv[14] - fixaff = sys.argv[15] - output = os.path.join(outfpath,outfname) - outpath = os.path.join(outfpath,title) - outprunepath = os.path.join(outfpath,'ldprune_%s' % title) - try: - os.makedirs(outfpath) - except: - pass - bfile = os.path.join(inpath,inbase) - outf = file(outfname,'w') - vcl = [plinke,'--noweb','--bfile',bfile,'--make-bed','--out', - outpath,'--set-hh-missing','--mind',mind, - '--geno',geno,'--maf',maf,'--hwe',hwe,'--me',me1,me2] - # yes - the --me parameter takes 2 values - mendels per snp and per family - if relf == 'oo': # plink filters are what they leave... - vcl.append('--filter-nonfounders') # leave only offspring - elif relf == 'fo': - vcl.append('--filter-founders') - if afff == 'affonly': - vcl.append('--filter-controls') - elif relf == 'unaffonly': - vcl.append('--filter-cases') - if sexf == 'fsex': - vcl.append('--filter-females') - elif relf == 'msex': - vcl.append('--filter-males') - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath) - retval = p.wait() - plog.append('%s started, called as %s' % (prog,' '.join(sys.argv))) - outf.write(galhtmlprefix % prog) - outf.write('<ul>\n') - plogf = '%s.log' % os.path.join(outfpath,title) - try: - plogl = file(plogf,'r').readlines() - plog += [x.strip() for x in plogl] - except: - plog += ['###Cannot open plink log file %s' % plogf,] - # if fixaff, want to 'fix' the fam file - if fixaff <> '0': - nchanged = fixoutaff(outpath=outpath,newaff=fixaff) - plog += ['## fixaff was requested %d subjects affection status changed to %s' % (nchanged,fixaff)] - pf = file(plogf,'w') - pf.write('\n'.join(plog)) - pf.close() - globme = os.path.join(outfpath,'*') - flist = glob.glob(globme) - flist.sort() - for i, data in enumerate( flist ): - outf.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1])) - outf.write('</ul>\n') - outf.write("</ul></br></div></body></html>") - outf.close() - - -if __name__ == "__main__": - clean() - diff -r 3df68022beef2077798ed50a33afb03be75a841a -r c8b55344e779e8be93bae5d66f52128addd83003 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ /dev/null @@ -1,155 +0,0 @@ -<tool id="rgClean1" name="Clean genotypes:"> - <requirements><requirement type="package">plink</requirement></requirements> - <description>filter markers, subjects</description> - - <command interpreter="python"> - rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' - '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path' - '$relfilter' '$afffilter' '$sexfilter' '$fixaff' - </command> - - <inputs> - <param name="input_file" type="data" label="RGenetics genotype library file in compressed Plink format" - size="120" format="pbed" /> - <param name="title" type="text" size="80" label="Descriptive title for cleaned genotype file" value="Cleaned_data"/> - <param name="geno" type="text" label="Maximum Missing Fraction: Markers" value="0.05" /> - <param name="mind" type="text" value="0.1" label="Maximum Missing Fraction: Subjects"/> - <param name="mef" type="text" label="Maximum Mendel Error Rate: Family" value="0.05"/> - <param name="mei" type="text" label="Maximum Mendel Error Rate: Marker" value="0.05"/> - <param name="hwe" type="text" value="0" label="Smallest HWE p value (set to 0 for all)" /> - <param name="maf" type="text" value="0.01" - label="Smallest Minor Allele Frequency (set to 0 for all)"/> - <param name='relfilter' label = "Filter on pedigree relatedness" type="select" - optional="false" size="132" - help="Optionally remove related subjects if pedigree identifies founders and their offspring"> - <option value="all" selected='true'>No filter on relatedness</option> - <option value="fo" >Keep Founders only (pedigree m/f ID = "0")</option> - <option value="oo" >Keep Offspring only (one randomly chosen if >1 sibs in family)</option> - </param> - <param name='afffilter' label = "Filter on affection status" type="select" - optional="false" size="132" - help="Optionally remove affected or non affected subjects"> - <option value="allaff" selected='true'>No filter on affection status</option> - <option value="affonly" >Keep Controls only (affection='1')</option> - <option value="unaffonly" >Keep Cases only (affection='2')</option> - </param> - <param name='sexfilter' label = "Filter on gender" type="select" - optional="false" size="132" - help="Optionally remove all male or all female subjects"> - <option value="allsex" selected='true'>No filter on gender status</option> - <option value="msex" >Keep Males only (pedigree gender='1')</option> - <option value="fsex" >Keep Females only (pedigree gender='2')</option> - </param> - <param name="fixaff" type="text" value="0" - label = "Change ALL subjects affection status to (0=no change,1=unaff,2=aff)" - help="Use this option to switch the affection status to a new value for all output subjects" /> - </inputs> - - <outputs> - <data format="pbed" name="out_file1" metadata_source="input_file" label="${title}_rgClean.pbed" /> - </outputs> - -<tests> - <test> - <param name='input_file' value='tinywga' ftype='pbed' > - <metadata name='base_name' value='tinywga' /> - <composite_data value='tinywga.bim' /> - <composite_data value='tinywga.bed' /> - <composite_data value='tinywga.fam' /> - <edit_attributes type='name' value='tinywga' /> - </param> - <param name='title' value='rgCleantest1' /> - <param name="geno" value="1" /> - <param name="mind" value="1" /> - <param name="mef" value="0" /> - <param name="mei" value="0" /> - <param name="hwe" value="0" /> - <param name="maf" value="0" /> - <param name="relfilter" value="all" /> - <param name="afffilter" value="allaff" /> - <param name="sexfilter" value="allsex" /> - <param name="fixaff" value="0" /> - <output name='out_file1' file='rgtestouts/rgClean/rgCleantest1.pbed' compare="diff" lines_diff="25" > - <extra_files type="file" name='rgCleantest1.bim' value="rgtestouts/rgClean/rgCleantest1.bim" compare="diff" /> - <extra_files type="file" name='rgCleantest1.fam' value="rgtestouts/rgClean/rgCleantest1.fam" compare="diff" /> - <extra_files type="file" name='rgCleantest1.bed' value="rgtestouts/rgClean/rgCleantest1.bed" compare="diff" /> - </output> - </test> -</tests> -<help> - -.. class:: infomark - -**Syntax** - -- **Genotype data** is the input genotype file chosen from your current history -- **Descriptive title** is the name to use for the filtered output file -- **Missfrac threshold: subjects** is the threshold for missingness by subject. Subjects with more than this fraction missing will be excluded from the import -- **Missfrac threshold: markers** is the threshold for missingness by marker. Markers with more than this fraction missing will be excluded from the import -- **MaxMendel Individuals** Mendel error fraction above which to exclude subjects with more than the specified fraction of mendelian errors in transmission (for family data only) -- **MaxMendel Families** Mendel error fraction above which to exclude families with more than the specified fraction of mendelian errors in transmission (for family data only) -- **HWE** is the threshold for HWE test p values below which the marker will not be imported. Set this to -1 and all markers will be imported regardless of HWE p value -- **MAF** is the threshold for minor allele frequency - SNPs with lower MAF will be excluded -- **Filters** for founders/offspring or affected/unaffected or males/females are optionally available if needed -- **Change Affection** is only needed if you want to change the affection status for creating new analysis datasets - ------ - -**Attribution** - -This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/, -and the R http://cran.r-project.org/ and -Bioconductor http://www.bioconductor.org/ projects. -respectively. - -In particular, http://pngu.mgh.harvard.edu/~purcell/plink/ -has excellent documentation describing the parameters you can set here. - -This implementation is a Galaxy tool wrapper around these third party applications. -It was originally designed and written for family based data from the CAMP Illumina run of 2007 by -ross lazarus (ross.lazarus(a)gmail.com) and incorporated into the rgenetics toolkit. - -Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy. - ------ - -**Summary** - -Reliable statistical inference depends on reliable data. Poor quality samples and markers -may add more noise than signal, decreasing statistical power. Removing the worst of them -can be done by setting thresholds for some of the commonly used technical quality measures -for genotype data. Of course discordant replicate calls are also very informative but are not -in scope here. - -Marker cleaning: Filters are available to remove markers below a specific minor allele -frequency, beyond a Hardy Wienberg threshold, below a minor allele frequency threshold, -or above a threshold for missingness. If family data are available, thresholds for Mendelian -error can be set. - -Subject cleaning: Filters are available to remove subjects with many missing calls. Subjects and markers for family data can be filtered by proportions -of Mendelian errors in observed transmission. Use the QC reporting tool to -generate a comprehensive series of reports for quality control. - -Note that ancestry and cryptic relatedness should also be checked using the relevant tools. - ------ - -.. class:: infomark - -**Tip** - -You can check that you got what you asked for by running the QC tool to ensure that the distributions -are truncated the way you expect. Note that you do not expect that the thresholds will be exactly -what you set - some bad assays and subjects are out in multiple QC measures, so you sometimes have -more samples or markers than you exactly set for each threshold. Finally, the ordering of -operations matters and Plink is somewhat restrictive about what it will do on each pass -of the data. At least it's fixed. - ------ - -This Galaxy tool was written by Ross Lazarus for the Rgenetics project -It uses Plink for most calculations - for full Plink attribution, source code and documentation, -please see http://pngu.mgh.harvard.edu/~purcell/plink/ plus some custom python code - -</help> -</tool> This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 07 Oct '13

07 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78eaaca131e3/ Changeset: 78eaaca131e3 User: dan Date: 2013-10-07 23:00:22 Summary: Fix for history updater when setting metadata Affected #: 1 file diff -r 4db4660f5b121eee69a822b9c1294e4316855715 -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -152,7 +152,8 @@ var timeout; // set up to keep pulling if this history in run/queue state if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.SETTING_METADATA )){ //|| ( history.hdas.running() ) ){ timeout = history.updateAfterDelay(); https://bitbucket.org/galaxy/galaxy-central/commits/f76c280cdee5/ Changeset: f76c280cdee5 User: dan Date: 2013-10-07 23:00:29 Summary: Pack scripts Affected #: 11 files diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return 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false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h)}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});$(".community_rating_star").rating({});make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$("<span>"+e+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(b,c){var a=$('input[name="id"]:checked').length;if(!a>0){return false}if(c!="None"&&c!=""){if(!confirm(c)){return false}}$("#operation").val(b.value);b.form.submit();return true}; \ No newline at end of file +jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$("<span>"+e+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(b,c){var a=$('input[name="id"]:checked').length;if(!a>0){return false}if(c!="None"&&c!=""){if(!confirm(c)){return false}}$("#operation").val(b.value);b.form.submit();return true}; \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",defaults:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b)}},show:function(c){if(c){this.create(c)}var b=(this.$el).find(".modal-body");b.css("max-height",$(document).height()/2);if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){c=_.defaults(c,this.defaults);if(c.body=="progress"){c.body='<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'}if(this.$el){this.$el.remove()}this.setElement(this.template(c.title));var b=(this.$el).find(".modal-body");var e=(this.$el).find(".modal-footer");var d=(this.$el).find(".buttons");b.append($(c.body));if(c.height){b.css("height",c.height)}if(c.buttons){$.each(c.buttons,function(f,g){d.append($('<button id="'+String(f).toLowerCase()+'"></button>').text(f).click(g)).append(" ")})}else{e.hide()}$(this.el_main).append($(this.el))},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+b+'</h3></span></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefaults:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b)}},show:function(c){this.initialize(c);var b=(this.$el).find(".modal-body");b.css("max-height",$(document).height()/2);if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){c=_.defaults(c,this.optionsDefault);if(c.body=="progress"){c.body='<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'}if(this.$el){this.$el.remove()}this.setElement(this.template(c.title));var b=(this.$el).find(".modal-body");var e=(this.$el).find(".modal-footer");var d=(this.$el).find(".buttons");b.append($(c.body));if(c.height){b.css("height",c.height)}if(c.buttons){$.each(c.buttons,function(f,g){d.append($('<button id="'+String(f).toLowerCase()+'"></button>').text(f).click(g)).append(" ")})}else{e.hide()}$(this.elMain).append($(this.el))},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return $(this.el).find(".modal-body").scrollTop()},template:function(b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+b+'</h3></span></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)});n.hide_modal()})}})},"View in new visualization":function(){var o=i+"/trackster?"+$.param(k);n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:o});n.hide_modal()}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("<td>").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k!==undefined&&i<k.length){if(k[i]==="str"||k==="list"){j.addClass("stringalign")}}}return j},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.Galaxy.modal.hide()},"View in saved visualization":function(){n.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:m,buttons:{Cancel:function(){n.Galaxy.modal.hide()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){n.Galaxy.modal.hide();var o=$(this).val();k.id=o;n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)})})}}})},"View in new visualization":function(){n.Galaxy.modal.hide();var o=i+"/trackster?"+$.param(k);n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:o})}}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.hide_modal();Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}})},"View in new visualization":function(){f.hide_modal();Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)||(h.get("state")===HistoryDatasetAssociation.STATES.SETTING_METADATA)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:"Configure",body:drawable.config.build_form(),buttons:{Cancel:h,OK:f}})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/filters.js --- a/static/scripts/packed/viz/trackster/filters.js +++ b/static/scripts/packed/viz/trackster/filters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){var f=c.extend;var a=function(g){this.manager=null;this.name=g.name;this.index=g.index;this.tool_id=g.tool_id;this.tool_exp_name=g.tool_exp_name};f(a.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var d=function(i,h,g){return $("<a/>").attr("href","javascript:void(0);").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(g)};var e=function(o){a.call(this,o);this.low=("low" in o?o.low:-Number.MAX_VALUE);this.high=("high" in o?o.high:Number.MAX_VALUE);this.min=("min" in o?o.min:Number.MAX_VALUE);this.max=("max" in o?o.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var k=function(p,q,r){p.click(function(){var w=q.text(),u=parseFloat(r.slider("option","max")),t=(u<=1?4:u<=1000000?u.toString().length:6),v=false,s=$(this).parents(".slider-row");s.addClass("input");if(r.slider("option","values")){t=2*t+1;v=true}q.text("");$("<input type='text'/>").attr("size",t).attr("maxlength",t).attr("value",w).appendTo(q).focus().select().click(function(x){x.stopPropagation()}).blur(function(){$(this).remove();q.text(w);s.removeClass("input")}).keyup(function(B){if(B.keyCode===27){$(this).trigger("blur")}else{if(B.keyCode===13){var z=r.slider("option","min"),x=r.slider("option","max"),A=function(C){return(isNaN(C)||C>x||C<z)},y=$(this).val();if(!v){y=parseFloat(y);if(A(y)){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}else{y=y.split("-");y=[parseFloat(y[0]),parseFloat(y[1])];if(A(y[0])||A(y[1])){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}r.slider((v?"values":"value"),y);s.removeClass("input")}}})})};var h=this;h.parent_div=$("<div/>").addClass("filter-row slider-row");var g=$("<div/>").addClass("elt-label").appendTo(h.parent_div),m=$("<span/>").addClass("slider-name").text(h.name+" ").appendTo(g),i=$("<span/>").text(this.low+"-"+this.high),j=$("<span/>").addClass("slider-value").appendTo(g).append("[").append(i).append("]");h.values_span=i;var l=$("<div/>").addClass("slider").appendTo(h.parent_div);h.control_element=$("<div/>").attr("id",h.name+"-filter-control").appendTo(l);h.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(p,q){h.slide(p,q)},change:function(p,q){h.control_element.slider("option","slide").call(h.control_element,p,q)}});h.slider=h.control_element;h.slider_label=i;k(j,i,h.control_element);var n=$("<div/>").addClass("display-controls").appendTo(h.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){if(h.manager.alpha_filter!==h){h.manager.alpha_filter=h;h.manager.parent_div.find(".layer-transparent").removeClass("active").hide();h.transparency_icon.addClass("active").show()}else{h.manager.alpha_filter=null;h.transparency_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();this.height_icon=d("Use filter for data height","arrow-resize-090",function(){if(h.manager.height_filter!==h){h.manager.height_filter=h;h.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();h.height_icon.addClass("active").show()}else{h.manager.height_filter=null;h.height_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();h.parent_div.hover(function(){h.transparency_icon.show();h.height_icon.show()},function(){if(h.manager.alpha_filter!==h){h.transparency_icon.hide()}if(h.manager.height_filter!==h){h.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(h.parent_div)};f(e.prototype,{to_dict:function(){var g=a.prototype.to_dict.call(this);return f(g,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new e({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(i,g){var h=g-i;return(h<=2?0.01:1)},slide:function(i,j){var h=j.values;this.values_span.text(h[0]+"-"+h[1]);this.low=h[0];this.high=h[1];var g=this;setTimeout(function(){if(h[0]===g.low&&h[1]===g.high){g.manager.track.request_draw({force:true,clear_after:true})}},25)},applies_to:function(g){if(g.length>this.index){return true}return false},_keep_val:function(g){return(isNaN(g)||(g>=this.low&&g<=this.high))},keep:function(h){if(!this.applies_to(h)){return true}var k=this;var l=h[this.index];if(l instanceof Array){var j=true;for(var g=0;g<l.length;g++){if(!this._keep_val(l[g])){j=false;break}}return j}else{return this._keep_val(h[this.index])}},update_attrs:function(k){var g=false;if(!this.applies_to(k)){return g}var h=k[this.index];if(!(h instanceof Array)){h=[h]}for(var j=0;j<h.length;j++){var l=h[j];if(l<this.min){this.min=Math.floor(l);g=true}if(l>this.max){this.max=Math.ceil(l);g=true}}return g},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var h=this.slider.slider("option","min"),g=this.slider.slider("option","max");if(this.min<h||this.max>g){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var b=function(j,p){this.track=j;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(i){i.stopPropagation()}).click(function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()}).bind("keydown",function(i){i.stopPropagation()});if(p&&"filters" in p){var g=("alpha_filter" in p?p.alpha_filter:null),k=("height_filter" in p?p.height_filter:null),m=p.filters,h;for(var n=0;n<m.length;n++){if(m[n].type==="number"){h=new e(m[n]);this.add_filter(h);if(h.name===g){this.alpha_filter=h;h.transparency_icon.addClass("active").show()}if(h.name===k){this.height_filter=h;h.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in p&&p.visible){this.parent_div.show()}}if(this.filters.length!==0){var q=$("<div/>").addClass("param-row").appendTo(this.parent_div);var o=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(q);var l=this;o.click(function(){l.run_on_dataset()})}};f(b.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var k={},j=[],h;for(var g=0;g<this.filters.length;g++){h=this.filters[g];j.push(h.to_dict())}k.filters=j;k.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);k.height_filter=(this.height_filter?this.height_filter.name:null);k.visible=this.parent_div.is(":visible");return k},copy:function(h){var j=new b(h);for(var g=0;g<this.filters.length;g++){j.add_filter(this.filters[g].copy())}return j},add_filter:function(g){g.manager=this;this.parent_div.append(g.parent_div);this.filters.push(g)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.update_ui_elt()}},clear_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.slider.slider("option","values",[h.min,h.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var n=function(q,i,p){if(!(i in q)){q[i]=p}return q[i]};var m={},o,g;for(var l=0;l<this.filters.length;l++){o=this.filters[l];if(o.tool_id){if(o.min!==o.low){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" >= "+o.low}if(o.max!==o.high){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" <= "+o.high}}}var h=[];for(var k in m){h[h.length]=[k,m[k]]}(function j(u,r){var p=r[0],q=p[0],t=p[1],s="("+t.join(") and (")+")",i={cond:s,input:u,target_dataset_id:u,tool_id:q};r=r.slice(1);$.getJSON(run_tool_url,i,function(v){if(v.error){show_modal("Filter Dataset","Error running tool "+q,{Close:hide_modal})}else{if(r.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{j(v.dataset_id,r)}}})})(this.track.dataset_id,h)}});return{FiltersManager:b,NumberFilter:e}}); \ No newline at end of file +define(["libs/underscore"],function(c){var f=c.extend;var a=function(g){this.manager=null;this.name=g.name;this.index=g.index;this.tool_id=g.tool_id;this.tool_exp_name=g.tool_exp_name};f(a.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var d=function(i,h,g){return $("<a/>").attr("href","javascript:void(0);").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(g)};var e=function(o){a.call(this,o);this.low=("low" in o?o.low:-Number.MAX_VALUE);this.high=("high" in o?o.high:Number.MAX_VALUE);this.min=("min" in o?o.min:Number.MAX_VALUE);this.max=("max" in o?o.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var k=function(p,q,r){p.click(function(){var w=q.text(),u=parseFloat(r.slider("option","max")),t=(u<=1?4:u<=1000000?u.toString().length:6),v=false,s=$(this).parents(".slider-row");s.addClass("input");if(r.slider("option","values")){t=2*t+1;v=true}q.text("");$("<input type='text'/>").attr("size",t).attr("maxlength",t).attr("value",w).appendTo(q).focus().select().click(function(x){x.stopPropagation()}).blur(function(){$(this).remove();q.text(w);s.removeClass("input")}).keyup(function(B){if(B.keyCode===27){$(this).trigger("blur")}else{if(B.keyCode===13){var z=r.slider("option","min"),x=r.slider("option","max"),A=function(C){return(isNaN(C)||C>x||C<z)},y=$(this).val();if(!v){y=parseFloat(y);if(A(y)){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}else{y=y.split("-");y=[parseFloat(y[0]),parseFloat(y[1])];if(A(y[0])||A(y[1])){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}r.slider((v?"values":"value"),y);s.removeClass("input")}}})})};var h=this;h.parent_div=$("<div/>").addClass("filter-row slider-row");var g=$("<div/>").addClass("elt-label").appendTo(h.parent_div),m=$("<span/>").addClass("slider-name").text(h.name+" ").appendTo(g),i=$("<span/>").text(this.low+"-"+this.high),j=$("<span/>").addClass("slider-value").appendTo(g).append("[").append(i).append("]");h.values_span=i;var l=$("<div/>").addClass("slider").appendTo(h.parent_div);h.control_element=$("<div/>").attr("id",h.name+"-filter-control").appendTo(l);h.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(p,q){h.slide(p,q)},change:function(p,q){h.control_element.slider("option","slide").call(h.control_element,p,q)}});h.slider=h.control_element;h.slider_label=i;k(j,i,h.control_element);var n=$("<div/>").addClass("display-controls").appendTo(h.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){if(h.manager.alpha_filter!==h){h.manager.alpha_filter=h;h.manager.parent_div.find(".layer-transparent").removeClass("active").hide();h.transparency_icon.addClass("active").show()}else{h.manager.alpha_filter=null;h.transparency_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();this.height_icon=d("Use filter for data height","arrow-resize-090",function(){if(h.manager.height_filter!==h){h.manager.height_filter=h;h.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();h.height_icon.addClass("active").show()}else{h.manager.height_filter=null;h.height_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();h.parent_div.hover(function(){h.transparency_icon.show();h.height_icon.show()},function(){if(h.manager.alpha_filter!==h){h.transparency_icon.hide()}if(h.manager.height_filter!==h){h.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(h.parent_div)};f(e.prototype,{to_dict:function(){var g=a.prototype.to_dict.call(this);return f(g,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new e({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(i,g){var h=g-i;return(h<=2?0.01:1)},slide:function(i,j){var h=j.values;this.values_span.text(h[0]+"-"+h[1]);this.low=h[0];this.high=h[1];var g=this;setTimeout(function(){if(h[0]===g.low&&h[1]===g.high){g.manager.track.request_draw({force:true,clear_after:true})}},25)},applies_to:function(g){if(g.length>this.index){return true}return false},_keep_val:function(g){return(isNaN(g)||(g>=this.low&&g<=this.high))},keep:function(h){if(!this.applies_to(h)){return true}var k=this;var l=h[this.index];if(l instanceof Array){var j=true;for(var g=0;g<l.length;g++){if(!this._keep_val(l[g])){j=false;break}}return j}else{return this._keep_val(h[this.index])}},update_attrs:function(k){var g=false;if(!this.applies_to(k)){return g}var h=k[this.index];if(!(h instanceof Array)){h=[h]}for(var j=0;j<h.length;j++){var l=h[j];if(l<this.min){this.min=Math.floor(l);g=true}if(l>this.max){this.max=Math.ceil(l);g=true}}return g},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var h=this.slider.slider("option","min"),g=this.slider.slider("option","max");if(this.min<h||this.max>g){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var b=function(j,p){this.track=j;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(i){i.stopPropagation()}).click(function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()}).bind("keydown",function(i){i.stopPropagation()});if(p&&"filters" in p){var g=("alpha_filter" in p?p.alpha_filter:null),k=("height_filter" in p?p.height_filter:null),m=p.filters,h;for(var n=0;n<m.length;n++){if(m[n].type==="number"){h=new e(m[n]);this.add_filter(h);if(h.name===g){this.alpha_filter=h;h.transparency_icon.addClass("active").show()}if(h.name===k){this.height_filter=h;h.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in p&&p.visible){this.parent_div.show()}}if(this.filters.length!==0){var q=$("<div/>").addClass("param-row").appendTo(this.parent_div);var o=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(q);var l=this;o.click(function(){l.run_on_dataset()})}};f(b.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var k={},j=[],h;for(var g=0;g<this.filters.length;g++){h=this.filters[g];j.push(h.to_dict())}k.filters=j;k.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);k.height_filter=(this.height_filter?this.height_filter.name:null);k.visible=this.parent_div.is(":visible");return k},copy:function(h){var j=new b(h);for(var g=0;g<this.filters.length;g++){j.add_filter(this.filters[g].copy())}return j},add_filter:function(g){g.manager=this;this.parent_div.append(g.parent_div);this.filters.push(g)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.update_ui_elt()}},clear_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.slider.slider("option","values",[h.min,h.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var n=function(q,i,p){if(!(i in q)){q[i]=p}return q[i]};var m={},o,g;for(var l=0;l<this.filters.length;l++){o=this.filters[l];if(o.tool_id){if(o.min!==o.low){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" >= "+o.low}if(o.max!==o.high){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" <= "+o.high}}}var h=[];for(var k in m){h[h.length]=[k,m[k]]}(function j(u,r){var p=r[0],q=p[0],t=p[1],s="("+t.join(") and (")+")",i={cond:s,input:u,target_dataset_id:u,tool_id:q};r=r.slice(1);$.getJSON(run_tool_url,i,function(v){if(v.error){Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+q,buttons:{Close:Galaxy.modal.hide()}})}else{if(r.length===0){Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}})}else{j(v.dataset_id,r)}}})})(this.track.dataset_id,h)}});return{FiltersManager:b,NumberFilter:e}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ae.config.build_form(),buttons:{Cancel:ag,Ok:ad}})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){Galaxy.modal.show({title:ad.get("name")+" is Running",body:ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:af,buttons:{No:ai,Yes:ae}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ah.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ae.config.build_form(),buttons:{Cancel:ag,Ok:ad}})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){Galaxy.modal.show({title:ad.get("name")+" is Running",body:ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:af,buttons:{No:ai,Yes:ae}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ah.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}var ag=new (this.painter)(null,null,null,this.prefs,ah);return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ah,ai,ak,ae){N.prototype.postdraw_actions.call(this,ah,ai,ak,ae);var ag=ac.filter(ah,function(al){return(al instanceof M)});var af=this.dataset.get_metadata("sample_names");if(ag.length===0&&this.prefs.show_labels&&af){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var aj=af.join("<br/>");this.tiles_div.prepend($("<div/>").html(aj).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: Dave Bouvier: Fix for update manager functional test failing.
by commits-noreply＠bitbucket.org 07 Oct '13

07 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4db4660f5b12/ Changeset: 4db4660f5b12 User: Dave Bouvier Date: 2013-10-07 22:46:17 Summary: Fix for update manager functional test failing. Affected #: 2 files diff -r f3bdde9002def4b09eae778dbd250d40512a30ac -r 4db4660f5b121eee69a822b9c1294e4316855715 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1093,6 +1093,10 @@ self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def update_tool_shed_status( self ): + url = '/admin_toolshed/update_tool_shed_status_for_installed_repository?all_installed_repositories=True' + self.visit_galaxy_url( url ) + def upload_file( self, repository, filename, diff -r f3bdde9002def4b09eae778dbd250d40512a30ac -r 4db4660f5b121eee69a822b9c1294e4316855715 test/tool_shed/functional/test_1410_update_manager.py --- a/test/tool_shed/functional/test_1410_update_manager.py +++ b/test/tool_shed/functional/test_1410_update_manager.py @@ -121,5 +121,8 @@ time.sleep( 3 ) self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) - self.display_galaxy_browse_repositories_page( strings_displayed=[ 'state-color-running' ] ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.update_tool_shed_status() + strings_displayed = [ '"%s"><img src="/static/images/icon_warning_sml.gif"' % self.security.encode_id( repository.id ) ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix javascript function to check all check boxes for select lists in the tool shed and Galaxy that handle resetting metadata on selected repositories and installing and uninstalling selected tool dependencies.
by commits-noreply＠bitbucket.org 07 Oct '13

07 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3bdde9002de/ Changeset: f3bdde9002de User: greg Date: 2013-10-07 22:35:38 Summary: Fix javascript function to check all check boxes for select lists in the tool shed and Galaxy that handle resetting metadata on selected repositories and installing and uninstalling selected tool dependencies. Affected #: 4 files diff -r 09a383314143244d37b5d40a565e75b131dff2b5 -r f3bdde9002def4b09eae778dbd250d40512a30ac templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -39,7 +39,8 @@ trans.model.ToolDependency.installation_status.UNINSTALLED ]: can_install = True if not can_uninstall: - if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: + if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: can_uninstall = True %><tr> @@ -67,7 +68,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAllUninstalled" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllFields( 'uninstalled_tool_dependency_ids', 'checkAllUninstalled' );"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b> + <input type="checkbox" id="checkAllUninstalled" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllUninstalledToolDependencyIdFields(1);"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b></div><div style="clear: both"></div><div class="form-row"> @@ -88,7 +89,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAllInstalled" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllFields( 'inst_td_ids', 'checkAllInstalled' );"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b> + <input type="checkbox" id="checkAllInstalled" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllInstalledToolDependencyIdFields(1);"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b></div><div style="clear: both"></div><div class="form-row"> diff -r 09a383314143244d37b5d40a565e75b131dff2b5 -r f3bdde9002def4b09eae778dbd250d40512a30ac templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -24,7 +24,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b> + <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllRepositoryIdFields(1);"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row"> diff -r 09a383314143244d37b5d40a565e75b131dff2b5 -r f3bdde9002def4b09eae778dbd250d40512a30ac templates/webapps/tool_shed/common/common.mako --- a/templates/webapps/tool_shed/common/common.mako +++ b/templates/webapps/tool_shed/common/common.mako @@ -1,15 +1,7 @@ -<%def name="common_misc_javascripts( element_id=None )"> +<%def name="common_misc_javascripts()"><script type="text/javascript"> - function checkAllFields( name, element_id=element_id ) + function checkAllFields( chkAll, name ) { - if ( element_id ) - { - chkAll = document.getElementById( element_id ); - } - else - { - var chkAll = document.getElementById( 'checkAll' ); - } var checks = document.getElementsByTagName( 'input' ); var boxLength = checks.length; var allChecked = false; @@ -18,9 +10,9 @@ { for ( i=0; i < boxLength; i++ ) { - if ( checks[i].name.indexOf( name ) != -1 ) + if ( checks[ i ].name.indexOf( name ) != -1 ) { - checks[i].checked = true; + checks[ i ].checked = true; } } } @@ -28,13 +20,34 @@ { for ( i=0; i < boxLength; i++ ) { - if ( checks[i].name.indexOf( name ) != -1 ) + if ( checks[ i ].name.indexOf( name ) != -1 ) { - checks[i].checked = false + checks[ i ].checked = false; } } } } + + function checkAllRepositoryIdFields() + { + var chkAll = document.getElementById( 'checkAll' ); + var name = 'repository_ids'; + checkAllFields( chkAll, name ); + } + + function checkAllInstalledToolDependencyIdFields() + { + var chkAll = document.getElementById( 'checkAllInstalled' ); + var name = 'inst_td_ids'; + checkAllFields( chkAll, name ); + } + + function checkAllUninstalledToolDependencyIdFields() + { + var chkAll = document.getElementById( 'checkAllUninstalled' ); + var name = 'uninstalled_tool_dependency_ids'; + checkAllFields( chkAll, name ); + } </script></%def> diff -r 09a383314143244d37b5d40a565e75b131dff2b5 -r f3bdde9002def4b09eae778dbd250d40512a30ac templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako +++ b/templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako @@ -33,7 +33,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b> + <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllRepositoryIdFields(1);"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for auto-detect metadata tool running second set metadata call.
by commits-noreply＠bitbucket.org 07 Oct '13

07 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/09a383314143/ Changeset: 09a383314143 User: dan Date: 2013-10-07 22:27:08 Summary: Fix for auto-detect metadata tool running second set metadata call. Affected #: 3 files diff -r 3679add0809c669e752c913ade2fc8e45adcff46 -r 09a383314143244d37b5d40a565e75b131dff2b5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1495,6 +1495,12 @@ just copy these files directly to the ulimate destination. """ return output_path + + @property + def requires_setting_metadata( self ): + if self.tool: + return self.tool.requires_setting_metadata + return False class TaskWrapper(JobWrapper): diff -r 3679add0809c669e752c913ade2fc8e45adcff46 -r 09a383314143244d37b5d40a565e75b131dff2b5 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -176,7 +176,7 @@ # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior - if include_metadata: + if include_metadata and job_wrapper.requires_setting_metadata: commands += "; cd %s; " % os.path.abspath( os.getcwd() ) commands += job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), diff -r 3679add0809c669e752c913ade2fc8e45adcff46 -r 09a383314143244d37b5d40a565e75b131dff2b5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -971,6 +971,7 @@ """ tool_type = 'default' + requires_setting_metadata = True default_tool_action = DefaultToolAction dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) @@ -3134,6 +3135,8 @@ dataset. """ tool_type = 'set_metadata' + requires_setting_metadata = False + def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): for name, dataset in inp_data.iteritems(): external_metadata = JobExternalOutputMetadataWrapper( job ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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