November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Actually send error reports to the creator instead of lying and saying that we did.
by Bitbucket 07 Nov '11

07 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba739e96c1a1/ changeset: ba739e96c1a1 user: natefoo date: 2011-11-07 21:27:43 summary: Actually send error reports to the creator instead of lying and saying that we did. affected #: 1 file diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r ba739e96c1a14d649c37655cecfc5b835ab343d2 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -574,11 +574,9 @@ """ Sends an email. """ - header_to = to - if isinstance( to, list ): - header_to = ', '.join( to ) + to = listify( to ) msg = MIMEText( body ) - msg[ 'To' ] = header_to + msg[ 'To' ] = ', '.join( to ) msg[ 'From' ] = frm msg[ 'Subject' ] = subject if config.smtp_server is None: @@ -613,8 +611,6 @@ log.error( "No suitable authentication method was found: %s" % e ) s.close() raise - if isinstance( to, basestring ): - to = [ to ] s.sendmail( frm, to, msg.as_string() ) s.quit() 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: dannon: Fix bug introduced in 0ba260ea43c4 for displaying workflows.
by Bitbucket 07 Nov '11

07 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0cdd7bb67d95/ changeset: 0cdd7bb67d95 user: dannon date: 2011-11-07 18:46:14 summary: Fix bug introduced in 0ba260ea43c4 for displaying workflows. affected #: 1 file diff -r a6f7e5024f40ae2cb177c636e52c46962a3f0d91 -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -1,8 +1,8 @@ <%inherit file="/display_base.mako"/><%namespace file="/display_common.mako" import="render_message" /> -<% - from galaxy.tools.parameters import DataToolParameter, RuntimeValue +<%! + from galaxy.tools.parameters import DataToolParameter, RuntimeValue from galaxy.web import form_builder %> @@ -118,4 +118,4 @@ </tr> %endfor </table> -</%def> \ No newline at end of file +</%def> 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 implicit dataset conversion that was broken in 1827729ed37e.
by Bitbucket 07 Nov '11

07 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a6f7e5024f40/ changeset: a6f7e5024f40 user: dan date: 2011-11-07 17:19:07 summary: Fix for implicit dataset conversion that was broken in 1827729ed37e. affected #: 2 files diff -r 545288e40ee10ed48d422eb772b734ace1422451 -r a6f7e5024f40ae2cb177c636e52c46962a3f0d91 lib/galaxy/datatypes/display_applications/parameters.py --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -94,13 +94,11 @@ if target_ext and not converted_dataset: if isinstance( data, DisplayDataValueWrapper ): data = data.value - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - trans.sa_session.flush() - assoc.dataset = new_data + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) trans.sa_session.add( assoc ) trans.sa_session.flush() elif converted_dataset and converted_dataset.state == converted_dataset.states.ERROR: diff -r 545288e40ee10ed48d422eb772b734ace1422451 -r a6f7e5024f40ae2cb177c636e52c46962a3f0d91 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -43,13 +43,11 @@ data = converted_dataset else: #run converter here - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - trans.sa_session.flush() - assoc.dataset = new_data + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) trans.sa_session.add( assoc ) trans.sa_session.flush() data = new_data 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: 2 new changesets
by Bitbucket 05 Nov '11

05 Nov '11

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b80ca015c305/ changeset: b80ca015c305 user: jgoecks date: 2011-11-05 23:21:38 summary: Trackster: color reads based on strand aligned to. affected #: 2 files diff -r 21138a4a1fead60fd3c364658a1dabbde870646b -r b80ca015c305cc0768de10dbf60c38bd91abca50 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -462,8 +462,10 @@ # ID: feature[2], cigar, + # TODO? VCF does not have strand, so default to positive. + "+", new_seq, - float( feature[5] )] + float( feature[5] ) ] rval.append(payload) return { 'data': rval, 'message': message } @@ -609,11 +611,11 @@ data - a list of reads with the format [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] where <read_1> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] + [<start>, <end>, <cigar>, <strand>, ?<read_seq>?] and <read_2> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] + [<start>, <end>, <cigar>, <strand>, ?<read_seq>?] For single-end reads, read has format: - [<guid>, <start>, <end>, <name>, cigar, seq] + [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>] NOTE: read end and sequence data are not valid for reads outside of requested region and should not be used. @@ -641,17 +643,34 @@ else: return None + # Decode strand from read flag. + def decode_strand( read_flag, mask ): + strand_flag = ( read_flag & mask == 0 ) + if strand_flag: + return "+" + else: + return "-" + # Encode reads as list of lists. results = [] paired_pending = {} + unmapped = 0 for count, read in enumerate( data ): if count < start_val: continue - if count-start_val >= max_vals: + if ( count - start_val - unmapped ) >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "reads" ) break + + # If not mapped, skip read. + is_mapped = ( read.flag & 0x0004 == 0 ) + if not is_mapped: + unmapped += 1 + continue + qname = read.qname seq = read.seq + strand = decode_strand( read.flag, 0x0010 ) if read.cigar is not None: read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length else: @@ -664,14 +683,15 @@ pair['start'], read.pos + read_len, qname, - [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], - [ read.pos, read.pos + read_len, read.cigar, seq ] + [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], + [ read.pos, read.pos + read_len, read.cigar, strand, seq ] ] ) del paired_pending[qname] else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar } + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, + 'rlen': read_len, 'strand': strand, 'cigar': read.cigar } else: - results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] ) + results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, strand, read.seq] ) # Take care of reads whose mates are out of range. # TODO: count paired reads when adhering to max_vals? @@ -683,14 +703,14 @@ # Make read_1 start=end so that length is 0 b/c we don't know # read length. r1 = [ read['mate_start'], read['mate_start'] ] - r2 = [ read['start'], read['end'], read['cigar'], read['seq'] ] + r2 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] else: # Mate is after read. read_start = read['start'] # Make read_2 start=end so that length is 0 b/c we don't know # read length. Hence, end of read is start of read_2. read_end = read['mate_start'] - r1 = [ read['start'], read['end'], read['cigar'], read['seq'] ] + r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] r2 = [ read['mate_start'], read['mate_start'] ] results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] ) diff -r 21138a4a1fead60fd3c364658a1dabbde870646b -r b80ca015c305cc0768de10dbf60c38bd91abca50 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3580,11 +3580,15 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); + var + block_color = get_random_color(), + reverse_strand_color = get_random_color( [ block_color, "#ffffff" ] ); this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, - { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() }, + { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color }, { 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 }, @@ -4388,8 +4392,6 @@ this.ref_seq = (ref_seq ? ref_seq.data : null); }; -ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false }); - extend(ReadPainter.prototype, FeaturePainter.prototype, { /** * Returns height based on mode. @@ -4414,14 +4416,15 @@ /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { + draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) { ctx.textAlign = "center"; var track = this, tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, gap = 0, - char_width_px = ctx.canvas.manager.char_width_px; + char_width_px = ctx.canvas.manager.char_width_px, + block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color); // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -4468,7 +4471,7 @@ // Draw. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); if (gap > 0) { - ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = block_color; ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9); ctx.fillStyle = CONNECTOR_COLOR; // TODO: this can be made much more efficient by computing the complete sequence @@ -4486,7 +4489,7 @@ } } } else { - ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT); } @@ -4615,7 +4618,6 @@ f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, - block_color = this.prefs.block_color, label_color = this.prefs.label_color, // Left-gap for label text since we align chrom text to the position tick. gap = 0; @@ -4626,7 +4628,6 @@ } // Draw read. - ctx.fillStyle = block_color; if (feature[5] instanceof Array) { // Read is paired. var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ), @@ -4635,12 +4636,12 @@ b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ); // Draw left/forward read. - if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center); + 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]); } // Draw right/reverse read. if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center); + 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]); } // Draw connector. if (b2_start > b1_end) { @@ -4649,8 +4650,7 @@ } } else { // Read is single. - ctx.fillStyle = block_color; - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center); + 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 !== ".") { // Draw label. @@ -4664,7 +4664,6 @@ ctx.textAlign = "right"; ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8); } - ctx.fillStyle = block_color; } // FIXME: provide actual coordinates for drawn read. https://bitbucket.org/galaxy/galaxy-central/changeset/545288e40ee1/ changeset: 545288e40ee1 user: jgoecks date: 2011-11-06 00:12:07 summary: Trackster: tooltips for navigational elements and better showing/hiding of add tracks button. affected #: 2 files diff -r b80ca015c305cc0768de10dbf60c38bd91abca50 -r 545288e40ee10ed48d422eb772b734ace1422451 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -941,7 +941,7 @@ } }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); - this.location_span = $("<span/>").addClass("location").appendTo(this.nav_controls); + this.location_span = $("<span/>").addClass("location").attr('original-title', 'Click to change location').tipsy( { gravity: 'n' } ).appendTo(this.nav_controls); this.location_span.click(function() { view.location_span.hide(); view.chrom_select.hide(); @@ -953,8 +953,11 @@ if (this.vis_id !== undefined) { this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls); } - this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); - this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); + + this.zo_link = $("<a/>").attr("id", "zoom-out").attr("title", "Zoom out").tipsy( {gravity: 'n'} ) + .click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); + this.zi_link = $("<a/>").attr("id", "zoom-in").attr("title", "Zoom in").tipsy( {gravity: 'n'} ) + .click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); // Get initial set of chroms. this.load_chroms_deferred = this.load_chroms({low: 0}); @@ -1069,7 +1072,6 @@ this.reset(); $(window).trigger("resize"); - this.update_intro_div(); }, /** Add or remove intro div depending on view state. */ update_intro_div: function() { diff -r b80ca015c305cc0768de10dbf60c38bd91abca50 -r 545288e40ee10ed48d422eb772b734ace1422451 static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -111,6 +111,9 @@ } } + // Need to update intro div after drawables have been added. + view.update_intro_div(); + // Set overview. var overview_track; for (var i = 0; i < view.drawables.length; i++) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Use panels when adding a build from a new track browser.
by Bitbucket 03 Nov '11

03 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/21138a4a1fea/ changeset: 21138a4a1fea user: jgoecks date: 2011-11-03 21:54:45 summary: Use panels when adding a build from a new track browser. affected #: 1 file diff -r 6e286e6d1b0dda77ef2187aedee0ded555b1fe74 -r 21138a4a1fead60fd3c364658a1dabbde870646b templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako +++ b/templates/tracks/new_browser.mako @@ -19,7 +19,7 @@ </div><div class="form-row"> Is the build not listed here? - <a href="${h.url_for( controller='user', action='dbkeys', panels=True )}">Add a Custom Build</a> + <a href="${h.url_for( controller='user', action='dbkeys', use_panels=True )}">Add a Custom Build</a></div> %if default_dbkey is not None: <script type="text/javascript"> 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: Improve Cufflinks' documentation for gene annotation dataset parameters.
by Bitbucket 03 Nov '11

03 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6e286e6d1b0d/ changeset: 6e286e6d1b0d user: jgoecks date: 2011-11-03 21:45:44 summary: Improve Cufflinks' documentation for gene annotation dataset parameters. affected #: 1 file diff -r e96f8c994bb629cd0b3b0cb5387a6db84c7c2857 -r 6e286e6d1b0dda77ef2187aedee0ded555b1fe74 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -61,10 +61,10 @@ </param><when value="No"></when><when value="Use reference annotation"> - <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/></when><when value="Use reference annotation guide"> - <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/></when></conditional><conditional name="bias_correction"> 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: greg: Temporary work-arounds for dealing with Galaxy panels when switching from workflow UI and Galaxy UI.
by Bitbucket 03 Nov '11

03 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e96f8c994bb6/ changeset: e96f8c994bb6 user: greg date: 2011-11-03 21:23:59 summary: Temporary work-arounds for dealing with Galaxy panels when switching from workflow UI and Galaxy UI. affected #: 2 files diff -r 0622b489a0f17f4b328473a2930f335d8d879fa1 -r e96f8c994bb629cd0b3b0cb5387a6db84c7c2857 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -800,7 +800,7 @@ message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool…" ' - message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' + message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) diff -r 0622b489a0f17f4b328473a2930f335d8d879fa1 -r e96f8c994bb629cd0b3b0cb5387a6db84c7c2857 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1193,20 +1193,31 @@ # the Galaxy panels displayed whenever in Galaxy. message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" - for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): - if tool_shed_url.endswith( '/' ): - tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, trans.request.host ) + for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp ) for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] url += '&tool_id=%s' % missing_tool_id - message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' - return trans.response.send_redirect( web.url_for( controller='admin', - action='index', - webapp='galaxy', - message=message, - status=status ) ) + if local_file or tool_shed_url: + # Another Galaxy panels Hack: The request did not originate from the Galaxy + # workflow view, so we don't need to render the Galaxy panels. + return trans.response.send_redirect( web.url_for( controller='admin', + action='center', + webapp='galaxy', + message=message, + status=status ) ) + else: + # Another Galaxy panels hack: The request originated from the Galaxy + # workflow view, so we need to render the Galaxy panels. + return trans.response.send_redirect( web.url_for( controller='admin', + action='index', + webapp='galaxy', + message=message, + status=status ) ) else: # TODO: Figure out what to do here... pass 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: guru: Added 3 tools: 1) to compute weighted average values based on interval intersections (under Regional variation), 2) to perform logistic regression (under Multiple regression), 3) to compute partial R-squared (under Multiple regression).
by Bitbucket 03 Nov '11

03 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0622b489a0f1/ changeset: 0622b489a0f1 user: guru date: 2011-11-03 15:49:45 summary: Added 3 tools: 1) to compute weighted average values based on interval intersections (under Regional variation), 2) to perform logistic regression (under Multiple regression), 3) to compute partial R-squared (under Multiple regression). affected #: 13 files diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 test-data/interpolate_result.bed --- /dev/null +++ b/test-data/interpolate_result.bed @@ -0,0 +1,219 @@ +chr1 27800000 29750669 6600000 0 1.7386 +chr1 29800669 34400000 6600000 0 1.7920 +chr1 46500000 51300000 4800000 0 1.4004 +chr1 102000000 103636494 5000000 0 1.2007 +chr1 103686494 103843838 5000000 0 NA +chr1 103893838 107000000 5000000 0 1.1883 +chr1 117600000 120498679 3100000 0 1.4007 +chr1 120548679 120700000 3100000 0 NA +chr1 153300000 154800000 1500000 0 1.9511 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e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -175,6 +175,7 @@ <section name="Regional Variation" id="regVar"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> @@ -194,8 +195,10 @@ </section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /> + <tool file="regVariation/partialR_square.xml" /></section><section name="Multivariate Analysis" id="multVar"><tool file="multivariate_stats/pca.xml" /> diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/WeightedAverage.py --- /dev/null +++ b/tools/regVariation/WeightedAverage.py @@ -0,0 +1,103 @@ +#!/usr/bin/env python +""" + +usage: %prog bed_file_1 bed_file_2 out_file + -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file + -2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file +""" +from galaxy import eggs + +import collections +import sys, string +#import numpy +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +import sys, traceback, fileinput +from warnings import warn +from galaxy.tools.util.galaxyops import * +from bx.cookbook import doc_optparse + + +#export PYTHONPATH=~/galaxy/lib/ +#running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + + +def FindRate(chromosome,start_stop,dictType): + OverlapList=[] + for tempO in dictType[chromosome]: + DatabaseInterval=[tempO[0],tempO[1]] + Overlap=GetOverlap(start_stop,DatabaseInterval) + if Overlap>0: + OverlapList.append([Overlap,tempO[2]]) + + if len(OverlapList)>0: + + SumRecomb=0 + SumOverlap=0 + for member in OverlapList: + SumRecomb+=member[0]*member[1] + SumOverlap+=member[0] + averageRate=SumRecomb/SumOverlap + + return averageRate + + else: + return 'NA' + + + +def GetOverlap(a,b): + return min(a[1],b[1])-max(a[0],b[0]) + +options, args = doc_optparse.parse( __doc__ ) + +try: + chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 ) + chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 ) + input1, input2, input3 = args +except Exception, eee: + print eee + stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." ) + + + +fd2=open(input2) +lines2=fd2.readlines() +RecombChrDict=collections.defaultdict(list) + +skipped=0 +for line in lines2: + temp=line.strip().split() + try: + assert float(temp[int(name_col_2)]) + except: + skipped+=1 + continue + tempIndex=[int(temp[int(start_col_2)]),int(temp[int(end_col_2)]),float(temp[int(name_col_2)])] + RecombChrDict[temp[int(chr_col_2)]].append(tempIndex) + +print "Skipped %d features with invalid values" %(skipped) + +fd1=open(input1) +lines=fd1.readlines() +finalProduct='' +for line in lines: + temp=line.strip().split('\t') + chromosome=temp[int(chr_col_1)] + start=int(temp[int(start_col_1)]) + stop=int(temp[int(end_col_1)]) + start_stop=[start,stop] + RecombRate=FindRate(chromosome,start_stop,RecombChrDict) + try: + RecombRate="%.4f" %(float(RecombRate)) + except: + RecombRate=RecombRate + finalProduct+=line.strip()+'\t'+str(RecombRate)+'\n' +fdd=open(input3,'w') +fdd.writelines(finalProduct) +fdd.close() diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/WeightedAverage.xml --- /dev/null +++ b/tools/regVariation/WeightedAverage.xml @@ -0,0 +1,71 @@ +<tool id="wtavg" name="Assign weighted-average" version="1.0.0"> + <description> of the values of features overlapping an interval </description> + <command interpreter="python">WeightedAverage.py $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol}</command> + + <inputs> + <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/> + <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." /> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="genomic_interval" /> + </outputs> + <tests> +  + <test> + <param name="genomic_interval" value="interval_interpolate.bed"/> + <param name="genomic_feature" value="value_interpolate.bed"/> + <output name="out_file1" file="interpolate_result.bed"/> + </test> + + </tests> + <help> + + +.. class:: infomark + +**What it does** + +For each interval in your first dataset, this tool calculates the weighted average value of the overlapping features in your second dataset. + +- When a genomic interval partially or totally overlaps a single genomic feature, the value of that genomic feature is assigned to the genomic interval. +- When a genomic interval partially or totally overlaps with more than one genomic features, the average of the values of the overlapping genomic features weighted by the corresponding number of overlapping bases is assigned to the genomic interval. +- When a genomic interval does not overlap with any genomic feature, 'NA' will be assigned as it's value. + +----- + +.. class:: warningmark + +**Note** + +The input datasets should be in **bed** or **interval** format. Please use "edit attributes"/pencil icon to specify the column containing the values for the features in the second dataset as **name/identifier** column. + +The output will contain all the columns in the first input plus a new column containing the assigned value for each interval. + +----- + +**Example** + +- Suppose our first dataset contains the following **genomic intervals**:: + + chr start stop + chr1 1000 2000 + chr1 3000 5000 + chr1 8000 9000 + +- and our second dataset contains the following **genomic features** each having an associated value (in fourth column) :: + + chr start stop name + chr1 900 1200 0.5 + chr1 2900 3100 0.2 + chr1 4800 5100 0.8 + +- For each **genomic interval** in our first dataset, this tool calculates the weighted average value of the overlapping **genomic features** in our second dataset :: + + chr1 1000 2000 0.5 + chr1 3000 5000 0.6 + chr1 8000 9000 NA + + + +</help> +</tool> \ No newline at end of file diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/logistic_regression_vif.py --- /dev/null +++ b/tools/regVariation/logistic_regression_vif.py @@ -0,0 +1,185 @@ +#!/usr/bin/env python + +from galaxy import eggs +import sys, string +from rpy import * +import numpy + +#export PYTHONPATH=~/galaxy/lib/ + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() +#infile = 'logreg_inp.tab' +#y_col=3 +#x_cols=[1,2,3] +#outfile='logreg_out.txt' +#python logistic_regression_vif.py logreg_inp.tab 4 1,2,3 logreg_out2.tabular # running test +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] + + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') +elems = [] +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except: + yval = r('NA') + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except: + xval = r('NA') + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() + +check1=0 +check0=0 +for i in y_vals: + if i == 1: + check1=1 + if i == 0: + check0=1 +if check1==0 or check0==0: + sys.exit("Warning: logistic regression must have at least two classes") + +for i in y_vals: + if i not in [1,0,r('NA')]: + print >>fout, str(i) + sys.exit("Warning: the current version of this tool can run only with two classes and need to be labeled as 0 and 1.") + + +dat= r.list(x=array(x_vals1), y=y_vals) +novif=0 +set_default_mode(NO_CONVERSION) +try: + linear_model = r.glm(r("y ~ x"), data = r.na_exclude(dat),family="binomial") + #r('library(car)') + #r.assign('dat',dat) + #r.assign('ncols',len(x_cols)) + #r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')).as_py() + +except RException, rex: + stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.") +if len(x_cols)>1: + try: + + r('library(car)') + r.assign('dat',dat) + r.assign('ncols',len(x_cols)) + vif=r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')) + except RException, rex: + print rex +else: + novif=1 + +set_default_mode(BASIC_CONVERSION) + +coeffs=linear_model.as_py()['coefficients'] +null_deviance=linear_model.as_py()['null.deviance'] +residual_deviance=linear_model.as_py()['deviance'] +yintercept= coeffs['(Intercept)'] +summary = r.summary(linear_model) +co = summary.get('coefficients', 'NA') +""" +if len(co) != len(x_vals)+1: + stop_err("Stopped performing logistic regression on the input data, since one of the predictor columns contains only non-numeric or invalid values.") +""" + +try: + yintercept = r.round(float(yintercept), digits=10) + pvaly = r.round(float(co[0][3]), digits=10) +except: + pass +print >>fout, "response column\tc%d" %(y_col+1) +tempP=[] +for i in x_cols: + tempP.append('c'+str(i+1)) +tempP=','.join(tempP) +print >>fout, "predictor column(s)\t%s" %(tempP) +print >>fout, "Y-intercept\t%s" %(yintercept) +print >>fout, "p-value (Y-intercept)\t%s" %(pvaly) + +if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable + try: + slope = r.round(float(coeffs['x']), digits=10) + except: + slope = 'NA' + try: + pval = r.round(float(co[1][3]), digits=10) + except: + pval = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[0]+1,slope) + print >>fout, "p-value (c%d)\t%s" %(x_cols[0]+1,pval) +else: #Multiple regression case with >1 predictors + ind=1 + while ind < len(coeffs.keys()): + try: + slope = r.round(float(coeffs['x'+str(ind)]), digits=10) + except: + slope = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,slope) + try: + pval = r.round(float(co[ind][3]), digits=10) + except: + pval = 'NA' + print >>fout, "p-value (c%d)\t%s" %(x_cols[ind-1]+1,pval) + ind+=1 + +rsq = summary.get('r.squared','NA') + + +try: + rsq= r.round(float((null_deviance-residual_deviance)/null_deviance), digits=5) + null_deviance= r.round(float(null_deviance), digits=5) + residual_deviance= r.round(float(residual_deviance), digits=5) + + #rsq = r.round(float(rsq), digits=5) + +except: + pass + +print >>fout, "Null deviance\t%s" %(null_deviance) +print >>fout, "Residual deviance\t%s" %(residual_deviance) +print >>fout, "pseudo R-squared\t%s" %(rsq) +print >>fout, "\n" +print >>fout, 'vif' + +if novif==0: + py_vif=vif.as_py() + count=0 + for i in sorted(py_vif.keys()): + print >>fout,'c'+str(x_cols[count]+1) ,str(py_vif[i]) + count+=1 +elif novif==1: + print >>fout, "vif can calculate only when model have more than 1 predictor" diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/logistic_regression_vif.xml --- /dev/null +++ b/tools/regVariation/logistic_regression_vif.xml @@ -0,0 +1,74 @@ +<tool id="LogisticRegression" name="Perform Logistic Regression with vif" version="1.0.1"> + <description></description> + <command interpreter="python"> + logistic_regression_vif.py + $input1 + $response_col + $predictor_cols + $out_file1 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" numerical="True"/> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" numerical="True" multiple="true" > + <validator type="no_options" message="Please select at least one column."/> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> + <test> + <param name="input1" value="logreg_inp.tabular"/> + <param name="response_col" value="4"/> + <param name="predictor_cols" value="1,2,3"/> + <output name="out_file1" file="logreg_out2.tabular"/> + + </test> + </tests> + <help> + + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool uses the **'glm'** function from R statistical package to perform logistic regression on the input data. It outputs one file containing the summary statistics of the performed regression. Also, it calculates VIF(Variance Inflation Factor) with **'vif'** function from library (car) in R. + + +*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.* + +----- + +.. class:: warningmark + +**Note** + +- This tool currently treats all predictor variables as continuous numeric variables and response variable as categorical variable. Currently, the response variable can have only two classes, namely 0 and 1. The program will take 0 as base class. + +- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. + +- The summary statistics in the output are described below: + +- Pseudo R-squared: the proportion of model improvement from null model +- p-value: p-value for the z-test of the null hypothesis that the corresponding slope is equal to zero against the two-sided alternative. +- Coefficient indicates log ratio of (probability to be class 1 / probability to be class 0) + +- This tool also provides **Variance Inflation Factor or VIF** which quantifies the level of multicollinearity. The tool will automatic generate VIF if the model has more than one predictor. The higher the VIF, the higher is the multicollinearity. Multicollinearity will inflate standard error and reduce level of significance of the predictor. In the worst case, it can reverse direction of slope for highly correlated predictors if one of them is significant. A general thumb-rule is to use those predictors having VIF lower than 10 or 5. +- **vif** is calculated by + - First, regressing each predictor over all other predictors, and recording R-squared for each regression. + - Second, computing vif as 1/(1- R_squared) + + </help> +</tool> diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/partialR_square.py --- /dev/null +++ b/tools/regVariation/partialR_square.py @@ -0,0 +1,146 @@ +#!/usr/bin/env python + +from galaxy import eggs + +import sys, string +from rpy import * +import numpy + +#export PYTHONPATH=~/galaxy/lib/ +#running command python partialR_square.py reg_inp.tab 4 1,2,3 partialR_result.tabular + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def sscombs(s): + if len(s) == 1: + return [s] + else: + ssc = sscombs(s[1:]) + return [s[0]] + [s[0]+comb for comb in ssc] + ssc + + +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') + +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + """ + try: + float( elems[x_cols[k]] ) + except: + try: + msg = "This operation cannot be performed on non-numeric column %d containing value '%s'." %( col, elems[x_cols[k]] ) + except: + msg = "This operation cannot be performed on non-numeric data." + stop_err( msg ) + """ +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except Exception, ey: + yval = r('NA') + #print >>sys.stderr, "ey = %s" %ey + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except Exception, ex: + xval = r('NA') + #print >>sys.stderr, "ex = %s" %ex + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() +dat= r.list(x=array(x_vals1), y=y_vals) + +set_default_mode(NO_CONVERSION) +try: + full = r.lm(r("y ~ x"), data= r.na_exclude(dat)) #full model includes all the predictor variables specified by the user +except RException, rex: + stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.") +set_default_mode(BASIC_CONVERSION) + +summary = r.summary(full) +fullr2 = summary.get('r.squared','NA') + +if fullr2 == 'NA': + stop_error("Error in linear regression") + +if len(x_vals) < 10: + s = "" + for ch in range(len(x_vals)): + s += str(ch) +else: + stop_err("This tool only works with less than 10 predictors.") + +print >>fout, "#Model\tR-sq\tpartial_R_Terms\tpartial_R_Value" +all_combos = sorted(sscombs(s), key=len) +all_combos.reverse() +for j,cols in enumerate(all_combos): + #if len(cols) == len(s): #Same as the full model above + # continue + if len(cols) == 1: + x_vals1 = x_vals[int(cols)] + else: + x_v = [] + for col in cols: + x_v.append(x_vals[int(col)]) + x_vals1 = numpy.asarray(x_v).transpose() + dat= r.list(x=array(x_vals1), y=y_vals) + set_default_mode(NO_CONVERSION) + red = r.lm(r("y ~ x"), data= dat) #Reduced model + set_default_mode(BASIC_CONVERSION) + summary = r.summary(red) + redr2 = summary.get('r.squared','NA') + try: + partial_R = (float(fullr2)-float(redr2))/(1-float(redr2)) + except: + partial_R = 'NA' + col_str = "" + for col in cols: + col_str = col_str + str(int(x_cols[int(col)]) + 1) + " " + col_str.strip() + partial_R_col_str = "" + for col in s: + if col not in cols: + partial_R_col_str = partial_R_col_str + str(int(x_cols[int(col)]) + 1) + " " + partial_R_col_str.strip() + if len(cols) == len(s): #full model + partial_R_col_str = "-" + partial_R = "-" + try: + redr2 = "%.4f" %(float(redr2)) + except: + pass + try: + partial_R = "%.4f" %(float(partial_R)) + except: + pass + print >>fout, "%s\t%s\t%s\t%s" %(col_str,redr2,partial_R_col_str,partial_R) diff -r e13fb2823aa4cbd835de79c89f53feca37ab7969 -r 0622b489a0f17f4b328473a2930f335d8d879fa1 tools/regVariation/partialR_square.xml --- /dev/null +++ b/tools/regVariation/partialR_square.xml @@ -0,0 +1,68 @@ +<tool id="partialRsq" name="Compute partial R square" version="1.0.0"> + <description></description> + <command interpreter="python"> + partialR_square.py + $input1 + $response_col + $predictor_cols + $out_file1 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" /> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true"> + <validator type="no_options" message="Please select at least one column."/> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> +  + <test> + <param name="input1" value="regr_inp.tabular"/> + <param name="response_col" value="3"/> + <param name="predictor_cols" value="1,2"/> + <output name="out_file1" file="partialR_result.tabular"/> + </test> + + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool computes the Partial R squared for all possible variable subsets using the following formula: + +**Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, which denotes the case where the 'i'th predictor is dropped. + + + +In general, **Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, where, + +- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the full set of predictors SSE(X1, X2 … Xp) +- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the set of predictors excluding; for example, if we omit the first predictor, it will be SSE(X2 … Xp). + + +The 4 columns in the output are described below: + +- Column 1 (Model): denotes the variables present in the model +- Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1 +- Column 3 (Partial R squared_Terms): denotes the variable/s for which Partial R squared is computed. These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model. +- Column 4 (Partial R squared): denotes the Partial R squared value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model. + +*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.* + + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix bug I introduced when I made changes to eliminate the User Type select field if no real options exist because there are no required form definitions.
by Bitbucket 03 Nov '11

03 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e13fb2823aa4/ changeset: e13fb2823aa4 user: greg date: 2011-11-03 14:47:29 summary: Fix bug I introduced when I made changes to eliminate the User Type select field if no real options exist because there are no required form definitions. affected #: 2 files diff -r d04c852fd26a9792c5431da32072bbb62b07530e -r e13fb2823aa4cbd835de79c89f53feca37ab7969 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -65,7 +65,7 @@ ${subscribe_check_box.get_html()} </div> %endif - %if len( user_type_fd_id_select_field.options ) > 1: + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: <div class="form-row"><label>User type</label> ${user_type_fd_id_select_field.get_html()} diff -r d04c852fd26a9792c5431da32072bbb62b07530e -r e13fb2823aa4cbd835de79c89f53feca37ab7969 templates/webapps/galaxy/user/info.mako --- a/templates/webapps/galaxy/user/info.mako +++ b/templates/webapps/galaxy/user/info.mako @@ -13,7 +13,7 @@ <div class="toolForm"><form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User information</div> - %if len( user_type_fd_id_select_field.options ) > 1: + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: <div class="form-row"><label>User type:</label> ${user_type_fd_id_select_field.get_html()} 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: fix bug in showing 'add datasets' button and rename update_track_icons to update_icons for clarity.
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d04c852fd26a/ changeset: d04c852fd26a user: jgoecks date: 2011-11-02 23:05:38 summary: Trackster: fix bug in showing 'add datasets' button and rename update_track_icons to update_icons for clarity. affected #: 1 file diff -r 611ec861bde5a6c31eace77f94ab8024159cc77c -r d04c852fd26a9792c5431da32072bbb62b07530e static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -679,7 +679,7 @@ request_draw: function() {}, _draw: function() {}, to_json: function() {}, - update_track_icons: function() {}, + update_icons: function() {}, /** * Set drawable name. */ @@ -819,14 +819,14 @@ is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - this.update_track_icons(); + this.update_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { /** * Make popup menu for group. */ - update_track_icons: function() { + update_icons: function() { var group = this; var group_dropdown = {}; @@ -1073,7 +1073,7 @@ }, /** Add or remove intro div depending on view state. */ update_intro_div: function() { - if (this.num_tracks === 0) { + if (this.drawables.length === 0) { this.intro_div.appendTo(this.viewport_container); } else { @@ -2531,7 +2531,7 @@ } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; - track.update_track_icons(); + track.update_icons(); } track.content_div.text(DATA_OK); if (track.view.chrom) { @@ -2547,7 +2547,7 @@ } }); - this.update_track_icons(); + this.update_icons(); }, /** * Additional initialization required before drawing track for the first time. @@ -2625,7 +2625,7 @@ /** * Update track's buttons. */ - update_track_icons: function() { + update_icons: function() { var track = this; // @@ -3287,7 +3287,7 @@ if (!track.filters_available) { track.filters_div.hide(); } - track.update_track_icons(); + track.update_icons(); } } }, @@ -3601,7 +3601,7 @@ this.prefs = this.config.values; this.painter = painters.ReadPainter; - this.update_track_icons(); + this.update_icons(); }; extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); 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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