Mercurial > repos > frogs > frogs_3_1_0
view test-data/references/01-prepro-flash.html @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
| author | frogs |
|---|---|
| date | Thu, 28 Feb 2019 10:14:49 -0500 |
| parents | |
| children |
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<!DOCTYPE html> <!-- # Copyright (C) 2015 INRA # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <https://www.gnu.org/licenses/>. --> <html> <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> <meta name="version" content="r3.0-v1.0"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link> <style type="text/css"> #js-alert { width: 90%; margin-right: auto; margin-left: auto; } #content { width: 90%; margin-right: auto; margin-left: auto; } .clear { clear: both; height: 0px; width: 100%; float: none !important; } ul.nav-tabs { margin-bottom: 30px; } .page-item.active .page-link { z-index: 1; color: #fff; background-color: #8EADAC; border-color: #8EADAC; outline: none !important; box-shadow: none !important; } .btn { color: #fff; border:#8EADAC; background-color: #8EADAC; 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/** * Returns hash use to init HightChart line. * @param pTitle {String} The title of the chart. * @param pXTitle {String} The xAxis title. * @param pYTitle {String} The yAxis title. * @param pXCategories {Array} x scale labels. * @param pData {Array} The HightChart series. * @return {Hash} Parameters to use in Highchart's constructor. */ var lineplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) { return { chart: { type: 'line', zoomType: 'x', selectionMarkerFill: "rgb(222,159,115,0.25)" }, title: { text: pTitle }, xAxis: { title: { text: pXTitle } }, yAxis: { min: 0, title: { text: pYTitle } }, exporting:{buttons: {contextButton: { symbol: 'download' }}}, buttons: {contextButton: {menuItems: ['downloadPNG', 'downloadSVG']}}, navigation: { buttonOptions: { theme: { r: 4, fill:'#8EADAC', states: { hover: { fill: 'rgb(100, 138, 137)', stroke:'#8EADAC' }, select: { stroke: '#8EADAC', fill: 'rgb(100, 138, 137)', } } } } }, series: pData, tooltip: { formatter:function() { tooltip_head = '<b>Length ' + this.x + 'nt</b>' ; 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$.each(this.points, function(i, point) { s += '<br/>'+ '<span style="color: ' + point.series.color + '"> ' + point.series.name +' : </span>'+ point.y + " " + unity; sum += point.y; } ); s += '<br/>total : '+ sum + ' (' + Number(Math.round(sum*100/nb + "e+2") + "e-2") + '%)' return s; }, shared: true, useHTML: true }, plotOptions: { column: { stacking: 'normal', dataLabels: { enabled: true, style: { textShadow: false, color: (Highcharts.theme && Highcharts.theme.textColor) || 'white' } }, pointPadding: 0.2, borderWidth: 0 } }, credits: { enabled: false }, series: pSeries }; return param ; } /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// // // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// var filters_categories = ["before process", "paired-end assembled", "with 5' primer", "with 3' primer", "with expected length", "without N"] ; /* Example: ["before process", "assembled", "with 5' primer", "with 3' primer", "with expected length", "without N"] */ var filters_by_sample = {"artificial combined": {"02": {"with expected length": 12500, "with 3' primer": 12500, "with 5' primer": 12500, "without N": 12500, "paired-end assembled": 12500}, "03": {"with expected length": 12536, "with 3' primer": 12536, "with 5' primer": 12536, "without N": 12536, "paired-end assembled": 12536}, "01": {"with expected length": 12378, "with 3' primer": 12378, "with 5' primer": 12378, "without N": 12378, "paired-end assembled": 12378}}, "before process": {"02": 30000, "03": 30000, "01": 30000}, "merged": {"02": {"with expected length": 17500, "with 3' primer": 17500, "with 5' primer": 17500, "without N": 17500, "paired-end assembled": 17500}, "03": {"with expected length": 17464, "with 3' primer": 17464, "with 5' primer": 17464, "without N": 17464, "paired-end assembled": 17464}, "01": {"with expected length": 17622, "with 3' primer": 17622, "with 5' primer": 17622, "without N": 17622, "paired-end assembled": 17622}}} ; /* Example: var filters_by_sample = { "artificial combined": { "sampleA": {"with 3' primer": 100, "without N": 100, "with 5' primer": 200, "assembled": 300}, "sampleB": {"with 3' primer": 0, "without N": 0, "with 5' primer": 0, "assembled": 0}}, "combined": { "sampleA": {"with expected length": 997, "with 3' primer": 997, "without N": 997, "with 5' primer": 997, "assembled": 1000}, "sampleB": {"with expected length": 634, "with 3' primer": 727, "without N": 619, "with 5' primer": 800, "assembled": 834}}, "before process": {"sampleA": 1300, "sampleB": 834} } ; */ var before_lengths_by_sample = {"02": {"319": 291, "318": 607, "338": 1, "423": 297, "335": 316, "334": 2, "337": 302, "336": 345, "331": 286, "333": 315, "332": 3, "270": 101, "271": 146, "272": 457, "274": 296, "275": 615, "276": 588, "277": 319, "278": 326, "279": 6, "289": 2, "365": 1, "320": 607, "322": 1, "345": 298, "346": 314, "347": 2, "324": 1244, "369": 1, "281": 625, "280": 10, "364": 326, "422": 1, "285": 662, "349": 2, "287": 5, "309": 299, "303": 300, "298": 7, "300": 287, "301": 325, "302": 7, "325": 2, "304": 606, "305": 1, "306": 7, "307": 1, "299": 959, "363": 3, "267": 18, "358": 298, "269": 27, "268": 9, "321": 620, "282": 1222, "296": 881, "284": 300, "357": 2, "354": 2, "353": 306, "351": 1, "350": 330, "371": 2, "370": 315, "294": 311, "295": 5, "292": 2, "293": 2, "290": 1, "291": 322}, "03": {"319": 288, "318": 640, "338": 1, "423": 294, "335": 317, "334": 1, "337": 282, "336": 292, "331": 338, "330": 4, "333": 313, "270": 66, "271": 126, "272": 450, "274": 292, "275": 592, "276": 629, "277": 319, "278": 290, "279": 1, "289": 2, "345": 297, "320": 600, "322": 3, "323": 2, "346": 336, "321": 617, "324": 1162, "369": 2, "281": 617, "280": 8, "364": 323, "282": 1264, "285": 660, "284": 331, "287": 5, "309": 282, "358": 282, "300": 327, "301": 295, "302": 4, "303": 335, "304": 656, "306": 1, "307": 3, "299": 894, "267": 26, "370": 344, "269": 36, "268": 20, "283": 1, "317": 1, "365": 4, "349": 5, "357": 2, "354": 1, "353": 319, "352": 1, "298": 6, "350": 305, "296": 939, "297": 2, "294": 303, "295": 3, "290": 4, "291": 299}, "01": {"319": 285, "318": 592, "335": 322, "334": 2, "337": 292, "336": 292, "331": 301, "330": 6, "333": 294, "332": 1, "270": 75, "271": 137, "272": 489, "274": 293, "275": 625, "276": 608, "277": 268, "278": 340, "296": 974, "289": 3, "345": 323, "320": 660, "364": 309, "322": 1, "323": 3, "346": 291, "347": 1, "324": 1280, "369": 1, "281": 619, "280": 5, "423": 293, "282": 1299, "285": 606, "284": 309, "287": 7, "286": 1, "309": 315, "283": 2, "300": 331, "301": 297, "302": 5, "303": 303, "304": 592, "305": 3, "306": 5, "307": 2, "363": 1, "267": 22, "325": 2, "370": 337, "269": 28, "268": 13, "321": 600, "422": 1, "359": 2, "350": 324, "292": 1, "424": 1, "357": 1, "353": 329, "352": 2, "298": 4, "299": 951, "371": 2, "297": 1, "349": 2, "358": 308, "294": 301, "293": 1, "290": 7, "291": 319}} ; /* Example: { "sampleA": {"395": 1, "381": 192, "382": 1790, "383": 2903, "384": 1078, "385": 10536, "386": 18182, "387": 8613, "388": 1097, "389": 7}, "sampleB": {} } */ var after_lengths_by_sample = {"02": {"151": 1, "216": 1, "318": 1, "213": 5, "210": 1, "211": 2, "313": 314, "312": 298, "337": 315, "242": 611, "317": 330, "330": 3, "193": 1, "332": 1, "270": 300, "271": 606, "258": 322, "259": 2, "238": 142, "239": 456, "276": 299, "226": 2, "252": 661, "235": 9, "236": 27, "251": 299, "250": 1, "265": 3, "198": 7, "234": 9, "237": 101, "272": 1, "249": 1219, "248": 621, "289": 1, "288": 620, "320": 306, "321": 2, "268": 325, "331": 326, "324": 2, "325": 298, "233": 9, "285": 607, "287": 607, "286": 291, "243": 588, "202": 4, "300": 315, "301": 2, "302": 316, "303": 345, "304": 302, "305": 1, "316": 1, "263": 881, "244": 308, "261": 311, "260": 2, "241": 294, "266": 959, "229": 4, "228": 1, "389": 1, "225": 4, "219": 4, "223": 11, "222": 10, "221": 6, "220": 9, "245": 316, "338": 2, "218": 2, "262": 5, "314": 2, "247": 1, "336": 1, "390": 297, "215": 1, "298": 286, "299": 3, "267": 287, "292": 2, "194": 7, "291": 1244}, "03": {"216": 5, "151": 3, "319": 1, "215": 2, "198": 4, "210": 3, "211": 2, "313": 336, "312": 297, "337": 344, "242": 588, "331": 323, "316": 2, "193": 3, "332": 4, "270": 335, "271": 656, "258": 299, "390": 294, "238": 122, "239": 448, "276": 282, "252": 658, "235": 20, "236": 36, "251": 326, "257": 1, "233": 8, "213": 5, "234": 18, "237": 66, "249": 1264, "248": 611, "289": 3, "288": 617, "320": 319, "321": 1, "268": 295, "324": 2, "325": 282, "250": 1, "170": 3, "285": 640, "284": 1, "287": 600, "286": 288, "243": 629, "202": 3, "300": 313, "301": 1, "302": 317, "303": 292, "304": 282, "305": 1, "245": 278, "244": 310, "261": 303, "267": 327, "266": 894, "229": 4, "264": 2, "226": 1, "225": 4, "219": 6, "223": 9, "222": 12, "221": 1, "220": 8, "317": 305, "263": 939, "262": 3, "265": 3, "336": 2, "228": 2, "298": 338, "241": 291, "297": 1, "194": 1, "290": 2, "291": 1162}, "01": {"216": 3, "215": 3, "213": 7, "210": 5, "211": 3, "218": 1, "289": 1, "288": 600, "285": 592, "287": 660, "286": 285, "263": 974, "261": 301, "260": 1, "267": 331, "266": 951, "265": 1, "264": 1, "269": 1, "268": 297, "298": 301, "299": 1, "297": 2, "292": 2, "290": 3, "291": 1280, "319": 2, "198": 4, "313": 291, "312": 323, "317": 324, "316": 1, "193": 2, "314": 1, "270": 303, "271": 592, "272": 3, "390": 293, "276": 315, "300": 294, "301": 2, "302": 322, "303": 292, "304": 292, "245": 325, "244": 262, "247": 1, "241": 292, "243": 608, "242": 623, "389": 1, "249": 1298, "248": 618, "338": 2, "337": 337, "336": 1, "331": 309, "330": 1, "258": 319, "259": 1, "252": 603, "253": 1, "250": 2, "251": 306, "257": 2, "170": 4, "194": 5, "229": 1, "228": 2, "226": 1, "225": 2, "223": 6, "222": 15, "220": 5, "391": 1, "151": 1, "238": 136, "239": 487, "234": 15, "235": 13, "236": 28, "237": 75, "233": 7, "320": 329, "326": 2, "324": 1, "325": 308, "202": 3}} ; /* Example: { "sampleA": {"395": 1, "381": 192, "382": 1790, "383": 2903, "384": 1078, "385": 10536, "386": 18182, "387": 8613, "388": 1097, "389": 7}, "sampleB": {} } */ /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// // // Main // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /** * Disables/enables buttons in datatable. */ var updateButtonState = function(){ $("#display-spl-lengths").prop( "disabled", false ); if( $('input[id^="filterBySample-chk-"]:checked').length == 0 ){ $("#display-spl-lengths").prop( "disabled", true ); } $("#display-after-spl-lengths").prop( "disabled", false ); if( $('input[id^="filterBySample-chk-"]:checked').length == 0 ){ $("#display-after-spl-lengths").prop( "disabled", true ); } } /** * Draws for the selected sample(s) the line chart that represents the number of sequences by sequence length. */ var setLengthsGraph = function(lengths_by_sample,title){ var selected_series = new Array(); $('input[id^="filterBySample-chk-"]').each( function(){ if( $(this).is(':checked')){ var sample_name = $(this).prop('id').substring(19, $(this).prop('id').length) ; // Find min and max for the sample var min_length = null ; var max_length = null ; for(seq_length in lengths_by_sample[sample_name]){ if( max_length === null ){ min_length = parseInt(seq_length) ; max_length = parseInt(seq_length) ; } else { min_length = Math.min( min_length, parseInt(seq_length) ); max_length = Math.max( max_length, parseInt(seq_length) ); } } // Complete data var sample_data = new Array(); if( max_length !== null ){ for( var curr_length = min_length ; curr_length <= max_length ; curr_length++ ){ if( lengths_by_sample[sample_name].hasOwnProperty(curr_length.toString()) ){ sample_data.push([ curr_length, lengths_by_sample[sample_name][curr_length.toString()] ]); } else { sample_data.push( [curr_length, null] ); } } } // Add serie selected_series.push({ "name": sample_name, "data": sample_data }); } }); // Draw chart $('#lengths-chart').highcharts( lineplot_param(title, "Length", "Nb sequences", null, selected_series) ); } /** * Draws the bar chart that represents the total number of sequences after each filter. */ var summaryLoad = function(){ var total_input = 0; var extended_data = new Array(); var non_overlapped_data = new Array(); for( var spl_name in filters_by_sample["merged"] ){ total_input += filters_by_sample["before process"][spl_name] ; for ( var cat_idx = 1 ; cat_idx < filters_categories.length ; cat_idx++ ){ var cat = filters_categories[cat_idx] ; if(extended_data.length <= cat_idx-1){ extended_data.push(0); non_overlapped_data.push(0); } if (cat in filters_by_sample["merged"][spl_name]){ extended_data[cat_idx-1] += filters_by_sample["merged"][spl_name][cat] ; }else{ extended_data[cat_idx-1] = extended_data[cat_idx-2] ; } if ("artificial combined" in filters_by_sample) { if ( cat in filters_by_sample["artificial combined"][spl_name] ){ non_overlapped_data[cat_idx-1] += filters_by_sample["artificial combined"][spl_name][cat] ; }else{ non_overlapped_data[cat_idx-1] = non_overlapped_data[cat_idx-2] ; } } } } var global_series = [ { name: 'merged', data: extended_data }] if ("artificial combined" in filters_by_sample) { global_series.push({name: 'artificial combined', data: non_overlapped_data}); } $('#filter-summary').highcharts( histogram_param('Summary', total_input, 'Nb sequences', filters_categories.slice(0-filters_categories.length+1), global_series, 'seq') ); } /** * Set the table that represents by sample the number of sequences after each filter. * Use key to select one subhashtable */ var sampleDetailsLoad = function(key, checkBox, tableId, distrib_length){ // Table titles if (checkBox){ var titles = [ '<label class="container"><input id="filterBySample-check-all" type="checkbox" value="1"><span class="checkmark"></span></label>', "Samples"]; }else{ var titles = ["Samples"]; } titles.push( '% kept' ); var filters = filters_by_sample[key] ; for( var sample_name in filters ){ if (checkBox) { var sample_data = ['<label class="container"><input id="filterBySample-chk-' + sample_name + '" type="checkbox" value="1"><span class="checkmark"></span></label>', sample_name]; }else{ var sample_data = [sample_name]; } var last_idx = 0; for ( var cat_idx = 0 ; cat_idx < filters_categories.length ; cat_idx++ ){ var cat = filters_categories[cat_idx] ; if ( cat in filters[sample_name]) { last_idx = cat_idx if (!( titles.includes(cat) )){ titles.push(cat); } sample_data.push( numberDisplay(filters[sample_name][cat]) ); } } var prct_kept = filters[sample_name][filters_categories[last_idx]]*100/filters[sample_name][filters_categories[1]] if (isNaN(prct_kept)){ prct_kept = 0 } if (checkBox) { sample_data.splice(2, 0, numberDisplay(prct_kept)); }else{ sample_data.splice(1, 0, numberDisplay(prct_kept)); } $('#'+tableId+' tbody').append( '<tr><td>' + sample_data.join("</td><td>") + '</td></tr>' ); } $('#'+tableId+' thead').append( '<tr><th>' + titles.join("</th><th>") + '</th></tr>' ); $('#'+tableId+' .title').attr( "colspan", titles.length ); $('#'+tableId+' tfoot th').each(function(){ $(this).attr( "colspan", titles.length ); }); // Check all management $('#filterBySample-check-all').on('change', function (e) { // Manage check all if( $(this).is(':checked') ){ $('input[id^="filterBySample-chk-"]').each( function(){ $(this).prop( 'checked', true ); }); } else { $('input[id^="filterBySample-chk-"]').each( function(){ $(this).prop( 'checked', false ); }); } }); $('input[id^="filterBySample-chk-"]').on('change', function (e) { // Uncheck select all when uncheck one sample if( !$(this).is(':checked') && $('#filterBySample-check-all').is(':checked') ){ $('#filterBySample-check-all').prop( 'checked', false ); } }); // Buttons enable/disable management $('input[id^="filterBySample-check-all"]').on( 'change', updateButtonState ); $('input[id^="filterBySample-chk-"]').on( 'change', updateButtonState ); // Datatable var start_col_idx = 0 if(checkBox){ start_col_idx = 1 } $('#'+tableId+'').DataTable({ //"sDom": '<"top"<"#'+tableId+'-export"><"clear">lf>rt<"bottom"ip><"clear">', dom: "<'#"+tableId+"-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + "<'row'<'col-sm-12'tr>>" + "<'row'<'col-sm-5'i><'col-sm-7'p>>", 'order': [[start_col_idx, 'asc']], "pagingType": "simple", 'columnDefs': [{ 'targets': [0], 'orderable': false }], "fnDrawCallback": updateButtonState }); // Datatable export $('#'+tableId+'-export').html( '<button id="btn-exp" class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' ); $('#'+tableId+'-export').addClass( 'dataTables_filter' ); if ( checkBox){ $('#'+tableId+'-export').datatableExport({ 'table_id': tableId, 'omitted_columns': [0] }); }else{ $('#'+tableId+'-export').datatableExport({ 'table_id': tableId, }); } // Add modal listener if (distrib_length){ $('#lengths-modal').on('shown.bs.modal', function (event) { var button = $(event.relatedTarget); // Button that triggered the modal var data_type = button.data('whatever'); if( data_type == "before-process" ){ setLengthsGraph(before_lengths_by_sample,"Amplicon length distribution before trimming and filtering"); } else { setLengthsGraph(after_lengths_by_sample,"Preprocessed Amplicon Length distribution"); } }); } } $(function() { // Remove alert $('#js-alert').remove(); $('#content').removeClass("hidden"); // Display summary summaryLoad(); // Display data by sample if ("merged" in filters_by_sample ){ sampleDetailsLoad("merged",true, "filterBySample-table-combined", true); }else{ $("#filterBySample-table-combined").remove(); } if ("artificial combined" in filters_by_sample ){ sampleDetailsLoad("artificial combined", false, "filterBySample-table-artificialCombined", false); }else{ $("#filterBySample-table-artificialCombined").prev("h2").remove(); $("#filterBySample-table-artificialCombined").remove(); } /*$("select").addClass("selectpicker"); $(".dataTables_length select").selectpicker({ style: 'btn-info', size: 2, width : '60px' }); $('.selectpicker').selectpicker('refresh'); //$('select').selectpicker('refresh'); */ }); </script> </head> <body> <!-- Alert --> <p id="js-alert" class="alert alert-warning"> javascript is needed to display data.<br /> If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view. </p> <!-- Content --> <div id="content" class="hidden"> <h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Preprocess summary</h2> <div id="filter-summary"></div> <div id="filter-log"> <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on merged sequences</h2> <table id="filterBySample-table-combined" class="table table-striped"> <thead> <!-- <tr> <th class="title">Filtering by sample : details on full length amplicon reads</th> </tr> --> </thead> <tbody></tbody> <tfoot> <tr> <th> <span class="table-action">With selection:</span> <button id="display-spl-lengths" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display amplicon lengths</span> </button> <button id="display-after-spl-lengths" class="btn table-action" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display preprocessed amplicon lengths</span></button> </th> </tr> </tfoot> </table> <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on artificial combined sequences</h2> <table id="filterBySample-table-artificialCombined" class="table table-striped"> <thead> </thead> <tbody></tbody> </table> </div> </div> <!-- Modals --> <div class="modal" id="lengths-modal" tabindex="-1" role="dialog" aria-hidden="true"> <div class="modal-dialog modal-lg"> <div class="modal-content"> <div class="modal-header"> <h4 class="modal-title">Amplicons lengths</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button> </div> <div class="modal-body"> <div id="lengths-chart"></div> </div> <div class="modal-footer"> <button class="btn table-action fusion-right" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button> </div> </div> </div> </div> </body> </html>