annotate test-data/references/09-normalisation.html @ 30:fce825ec2c84 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty
author oinizan
date Fri, 02 May 2025 07:44:22 +0000
parents 646bee69560f
children
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1 <!DOCTYPE html>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <html>
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19 <head>
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20 <title>FROGS Abundance Normalisation</title>
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21 <meta charset="UTF-8">
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22 <meta name="version" content="4.2.0">
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23 <!-- CSS -->
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24 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>
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25 <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>
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26 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">
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27 <style type="text/css">
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28 #js-alert {
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29 width: 90%;
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30 margin-right: auto;
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31 margin-left: auto;
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32 }
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33 #content {
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34 width: 90%;
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35 margin-right: auto;
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36 margin-left: auto;
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37 }
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38 #filter-delete {
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39 display: block;
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40 }
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41 .clear {
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42 clear: both;
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43 height: 0px;
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44 width: 100%;
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45 float: none !important;
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46 }
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47 ul.nav-tabs {
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48 margin-bottom: 30px;
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49 }
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51 .page-item.active .page-link {
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52 z-index: 1;
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53 color: #fff;
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54 background-color: #8EADAC;
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55 border-color: #8EADAC;
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56 }
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57
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58 .btn {
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59 color: #fff;
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60 border:#8EADAC;
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61 background-color: #8EADAC;
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62 }
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63 .btn:focus, .btn:active {
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64 outline: none !important;
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65 box-shadow: none !important;
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66 }
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67 .btn:hover:enabled{
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68 color: #fff;
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69 border:#648a89;
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70 background-color: #648a89;
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71 cursor:pointer !important;
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72 }
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73
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74 .pb-2, .py-2 {
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75 padding-bottom: 1.5rem !important;
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76 margin-bottom: 2rem !important;
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77 margin-top: 4rem !important;
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78 }
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79 .pb-2-first{
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80 padding-bottom: 1.5rem !important;
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81 margin-bottom: 2rem !important;
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82 margin-top: 1rem !important;
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83 }
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84 .nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{
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85 color: #fff;
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86 background-color: #8EADAF;
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87 border-color: #dee2e6 #dee2e6 #fff;
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88 }
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89 a {
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90 color: #8EAEAF;
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91 }
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92 a:hover{
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93 color:#648a89;
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94 }
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95
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96 /* ##### THEME FOR CHECKBOXES ##### */
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97 .container {
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98 position: relative;
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99 padding-left: 35px;
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100 margin-bottom: 12px;
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101 cursor: pointer;
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102 -webkit-user-select: none;
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103 -moz-user-select: none;
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104 -ms-user-select: none;
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105 user-select: none;
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106 }
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107
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108 /* Hide the browser's default checkbox */
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109 .container input {
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110 position: absolute;
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111 opacity: 0;
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112 cursor: pointer;
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113 }
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114
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115 /* Create a custom checkbox */
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116 .checkmark {
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117 position: absolute;
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118 top: 0;
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119 left: 0;
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120 height: 25px;
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121 width: 25px;
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122 background-color: #8EADAC;
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123 border-radius: 5px;
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124 opacity:0.65;
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125 }
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126
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127 /* On mouse-over, add a grey background color */
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128 .container:hover input ~ .checkmark {
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129 background-color: #648a89;
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130 }
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131
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132 /* When the checkbox is checked, add a blue background */
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133 .container input:checked ~ .checkmark {
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134 background-color: #8EADAC;
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135 opacity:1;
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136 }
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137
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138 /* Create the checkmark/indicator (hidden when not checked) */
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139 .checkmark:after {
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140 content: "";
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141 position: absolute;
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142 display: none;
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143 }
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144
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145 /* Show the checkmark when checked */
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146 .container input:checked ~ .checkmark:after {
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147 display: block;
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148 }
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149
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150 /* Style the checkmark/indicator */
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151 .container .checkmark:after {
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152 left: 9px;
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153 top: 5px;
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154 width: 5px;
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155 height: 10px;
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156 border: solid white;
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157 border-width: 0 3px 3px 0;
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158 -webkit-transform: rotate(45deg);
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159 -ms-transform: rotate(45deg);
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160 transform: rotate(45deg);
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161 }
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162 /* ##### END THEME CHECKBOXES ##### */
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163 .highcharts-button > path{
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164 stroke:#fff !important;
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165 fill:#8EADAC !important;
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166 }
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167 g.highcharts-button{
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168 cursor:pointer !important;
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169 }
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170 g.highcharts-button:hover{
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171 color: #fff;
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172 border:#648a89;
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173 background-color: #648a89;
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174 background-color: #648a89;
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175 cursor:pointer !important;
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176 }
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177
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178 </style>
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179 <!-- JS -->
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180 <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>
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181 <script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts.js"></script>
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182 <script type="text/javascript" src="https://code.highcharts.com/8.2.0/modules/exporting.js"></script>
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183 <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
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184 <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>
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185 <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js" integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T" crossorigin="anonymous"></script>
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186 <script type="text/javascript">
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187 /***************************************************************
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188 * Copyright notice
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189 *
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190 * (c) 2014 PF bioinformatique de Toulouse
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191 * All rights reserved
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192 *
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193 *
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194 * This script is an adaptation of the venny script developed by
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195 * Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
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196 * Oliveros, J.C. (2007) VENNY. An interactive tool for comparing
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197 * lists with Venn Diagrams.
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198 * http://bioinfogp.cnb.csic.es/tools/venny/index.html.
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199 * It is distributed under the terms of the GNU General Public
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200 * License as published by the Free Software Foundation; either
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201 * version 2 of the License, or (at your option) any later version.
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202 *
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203 * The GNU General Public License can be found at
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204 * http://www.gnu.org/copyleft/gpl.html.
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205 *
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206 * This script is distributed in the hope that it will be useful,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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207 * but WITHOUT ANY WARRANTY; without even the implied warranty of
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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208 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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209 * GNU General Public License for more details.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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210 *
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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211 * This copyright notice MUST APPEAR in all copies of the script!
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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212 ***************************************************************/
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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213 !function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]="&#160;",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
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id="resultC001100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111111"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label1"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label2"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label3"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label4"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label5"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label6"></div>',o+="</div>",t.html(o),j=new C2S(O,N),s("*[id^=resultC]").each(function(){s(this).html(0),s(this).addClass("number-empty"),s(this).css("font-size",B.fontSize),s(this).css("font-family",B.fontFamily)}),s("*[id^=label]").each(function(){s(this).css("font-family",B.fontFamily)});var c=z();"list"==c[0]?w():"count"==c[0]&&E(),null!=B.searchInput&&B.searchInput.keyup(function(){F(B.searchInput.val(),B.searchMinSize)}),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1]),B.exporting===!0&&S(t,e,c[0]),c[1]>=4&&_(t,c[1]),s(".number-black").hover(function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){var l=this.listnames,r=this;s("*[id^=label]").each(function(){l.indexOf(s(this).text())<0?s(this).css("opacity",.1):s(this).css("opacity",.6)}),s(".number-black").each(function(){this!=r&&s(this).css("opacity",.1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}},function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){{this.listnames}s("*[id^=label]").each(function(){s(this).css("opacity",.5)}),s(".number-black").each(function(){s(this).css("opacity",1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}}),s("#canvasEllipse").html(j.getSvg())}),this}}(jQuery);
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216 </script>
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217 <script type="text/javascript">
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218 /*
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219 * HTMLTable.js 0.1.0 - HTMLTable Library
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220 *
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221 * Copyright (c) 2015 Escudie Frederic
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222 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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223 */
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224 function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
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225
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226 /*
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227 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
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228 *
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229 * Copyright (c) 2015 Escudie Frederic
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230 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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231 */
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232 !function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
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233 </script>
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234 <script type="text/javascript">
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235 /**
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236 * Returns the string representation of the number.
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237 * @param pValue {Float} The number to process.
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238 * @return {String} The string representation (example: 12856892.11111 => 12,856,892.11).
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239 */
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240 var numberDisplay = function( pValue ){
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241 var new_val = "" ;
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242 if( ("" + pValue + "").indexOf(".") != -1 ){
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243 new_val = pValue.toFixed(2).replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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244 } else {
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245 new_val = pValue.toFixed().replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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246 }
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247 return new_val ;
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248 }
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249
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250 var chartplot = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) {
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251 var chart = {
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252 title: {
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253 text: pTitle
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254 },
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255 xAxis: {},
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256 yAxis: {
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257 title: {
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258 text: pYTitle
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259 }
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260 },
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261 series: pData,
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262 credits: {
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263 enabled: false
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264 },
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265 exporting:{buttons: {contextButton: { symbol: 'download' }}},
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266 buttons: {contextButton: {menuItems: ['downloadPNG', 'downloadSVG']}},
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267 navigation: {
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268 buttonOptions: {
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269 theme: {
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270 r: 4,
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271 fill:'#8EADAC',
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272 states: {
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273 hover: {
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274 fill: 'rgb(100, 138, 137)',
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275 stroke:'#8EADAC'
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276 },
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277 select: {
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278 stroke: '#8EADAC',
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279 fill: 'rgb(100, 138, 137)',
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280 }
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281 }
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282 }
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283 }
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284 }
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285 }
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286 if( pXCategories != null ){
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287 chart['xAxis']['categories'] = pXCategories ;
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288 }
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289 if( pXTitle != null ){
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290 chart['xAxis']['title'] = { text: pXTitle } ;
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291 }
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292 if( pData.length <= 1 ) {
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293 chart['legend'] = {'enabled': false};
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294 } else {
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295 chart['legend'] = {'enabled': true};
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296 }
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297 return chart ;
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298 }
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299
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300 var pie_param = function( pTitle, pData, unity ) {
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301 var series = [{
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302 type: 'pie',
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303 name: unity,
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304 data: pData
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305 }]
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306 var plot = chartplot( pTitle, null, null, null, series );
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307 plot['tooltip'] = {
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308 pointFormat: '{series.name}: <b>{point.percentage:.1f}%</b>'
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309 };
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310 plot['plotOptions'] = {
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311 pie: {
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312 allowPointSelect: true,
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313 cursor: 'pointer',
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314 dataLabels: {
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315 enabled: true,
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316 useHTML : true,
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317 formatter: function () {
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318 return this.point.name + ' : ' + numberDisplay(this.point.y);
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319 },
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320 style: {
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321 color: (Highcharts.theme && Highcharts.theme.contrastTextColor) || 'black'
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322 }
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323 }
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324 }
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325 };
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326 return plot ;
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327 };
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328
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329 /**
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330 * Returns the HTML table representation of the data.
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331 * @param pTitle {String} The title of the table.
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332 * @param pCategories {Array} The title of each column.
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333 * @param pData {Array} 2D matrix with row and column data.
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334 * @return {String} The HTML table representation.
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335 */
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336 var table = function( pTitle, pCategories, pData ) {
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337 // Header
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338 var table_header = '' ;
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339 var table_header_line = "" ;
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340 for(var idx = 0 ; idx < pCategories.length ; idx++){
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341 table_header_line += " <th>" + pCategories[idx] + "</th>\n" ;
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342 }
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343 table_header += " <tr>\n" + table_header_line + " </tr>\n" ;
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344 table_header = " <thead>\n" + table_header + " </thead>\n" ;
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345
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346 // Body
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347 var table_body = '' ;
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348 for(var data_idx = 0 ; data_idx < pData.length ; data_idx++){
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349 var table_body_row = "" ;
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350 for(var category_idx = 0 ; category_idx < pCategories.length ; category_idx++){
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351 if( typeof pData[data_idx][category_idx] === "number" ) {
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352 table_body_row += " <td>" + numberDisplay(pData[data_idx][category_idx]) + "</td>\n" ;
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353 } else {
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354 table_body_row += " <td>" + pData[data_idx][category_idx] + "</td>\n" ;
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355 }
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356 }
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357 table_body += " <tr>\n" + table_body_row + " </tr>\n" ;
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358 }
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359 table_body = " <tbody>\n" + table_body + " </tbody>\n" ;
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360
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361 return '<table class="table table-striped table-bordered">\n' + table_header + table_body + "</table>\n" ;
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362 };
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363
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diff changeset
364
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365 $(function() {
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366 var categories = ["Nb ASV before normalisation", "Nb ASV after normalisation"] ;
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367 var del_categories = ["Nb sequences"] ;
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368 var series_by_sample = [{"name": "01_subsample", "data": [55, 39]}, {"name": "02_subsample", "data": [55, 40]}, {"name": "03_subsample", "data": [55, 41]}] ;
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369 var del_by_sample = [] ;
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370 var remove_info = {"abundance_kept": 300, "abundance_removed": 74828, "nb_kept": 50, "nb_removed": 5} ;
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371
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372 // Remove alert
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373 $('#js-alert').remove();
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374 $('#content').removeClass("hidden");
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375
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376 // Radializes colors
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377 Highcharts.setOptions({
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378 colors : ['#8EADAC', '#DE9F73'] ,
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379 lang: {thousandsSep: ','}
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380 });
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381 Highcharts.SVGRenderer.prototype.symbols.download = function (x, y, w, h) {
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382 var path = [
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383 // Arrow stem
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384 'M', x + w * 0.5, y,
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385 'L', x + w * 0.5, y + h * 0.7,
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386 // Arrow head
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387 'M', x + w * 0.3, y + h * 0.5,
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388 'L', x + w * 0.5, y + h * 0.7,
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389 'L', x + w * 0.7, y + h * 0.5,
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390 // Box
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391 'M', x, y + h * 0.9,
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392 'L', x, y + h,
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393 'L', x + w, y + h,
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394 'L', x + w, y + h * 0.9
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395 ];
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396 return path;
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397 };
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398 /* Radial gradient ?*/
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399 Highcharts.getOptions().colors = Highcharts.map(Highcharts.getOptions().colors, function (color) {
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400 return {
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401 radialGradient: { cx: 0.5, cy: 0.3, r: 0.7 },
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402 stops: [
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403 [0, color],
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404 [1, Highcharts.Color(color).brighten(-0.1).get('rgb')] // darken
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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405 ]
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406 };
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407 });
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408
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409 // Display chimera remove data
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410 var nb_filtered_data = [
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411 ['Kept', remove_info['nb_kept']],
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412 ['Removed', remove_info['nb_removed']]
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413 ];
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414 $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') );
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415 var abundance_filtered_data = [
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416 ['Kept', remove_info['abundance_kept']],
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417 ['Removed', remove_info['abundance_removed']]
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418 ];
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419 $('#abundance-filtered').highcharts( pie_param('Abundance', abundance_filtered_data, 'Sequences') );
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420
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421
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422
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423 // Display data by sample
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424 var table_categories = categories.slice() ;
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425 var table_del_categories = del_categories.slice() ;
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426
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427 table_categories.unshift( "Sample" );
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428 table_del_categories.unshift( "Sample" );
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429
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430 var table_series = new Array();
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431 var table_del_series = new Array();
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432
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433 for( var spl_idx = 0 ; spl_idx < series_by_sample.length ; spl_idx++ ){
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434 var nb_by_step = series_by_sample[spl_idx]['data'].slice() ;
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435 nb_by_step.unshift( series_by_sample[spl_idx]['name'] );
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436 table_series.push( nb_by_step );
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437 };
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438 if (del_by_sample.length == 0) {
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439 document.getElementById('filter-delete').style.display = "none"
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440 } else {
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441 for( var spl_idx = 0 ; spl_idx < del_by_sample.length ; spl_idx++ ){
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442 var nb_by_step = del_by_sample[spl_idx]['data'].slice() ;
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443 nb_by_step.unshift( del_by_sample[spl_idx]['name'] );
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444 table_del_series.push( nb_by_step );
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445 }
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446 };
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447
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448 $('#filter-delete').append( table("Delete samples", table_del_categories, table_del_series) );
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449 $('#filter-delete table').prop( 'id', 'del-table' );
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450 $('#filter-delete table').DataTable({
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451 dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" +
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452 "<'row'<'col-sm-12'tr>>" +
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453 "<'row'<'col-sm-5'i><'col-sm-7'p>>"
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454 });
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455 $('#details-csv-export').html( '<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' );
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456 $('#details-csv-export').addClass( 'dataTables_filter' );
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457 $('#details-csv-export').datatableExport({
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458 'table_id': "del-table"
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459 });
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460
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461 $('#filter-log').append( table("Composition by sample", table_categories, table_series) );
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462 $('#filter-log table').prop( 'id', 'details-table' );
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463 $('#filter-log table').DataTable({
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464 dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + "<'row'<'col-sm-12'tr>>" +
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465 "<'row'<'col-sm-5'i><'col-sm-7'p>>"
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466 });
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467 $('#details-csv-export').html( '<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' );
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468 $('#details-csv-export').addClass( 'dataTables_filter' );
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469 $('#details-csv-export').datatableExport({
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470 'table_id': "details-table"
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471 });
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472 });
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473 </script>
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474 </head>
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475 <body>
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476 <p id="js-alert" class="alert alert-warning">
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477 javascript is needed to display data.<br />
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478 If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
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479 </p>
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480 <div id="content" class="hidden">
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481 <div id="filter-summary">
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482 <h2 class="pb-2 mt-4 mb-2 border-bottom">Normalisation summary
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483
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484 </h2>
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485 <div class="row">
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486 <div id="nb-filtered" class="col-md-6"></div>
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487 <div id="abundance-filtered" class="col-md-6"></div>
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488 </div>
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489 </div>
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490 <div id="filter-delete">
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491 <h2 class="pb-2 mt-4 mb-2 border-bottom">Kept samples (nb sequences < 100)</h2>
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492 </div>
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493 <div id="filter-log">
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494 <h2 class="pb-2 mt-4 mb-2 border-bottom"> Normalisation summary per samples</h2>
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495 </div>
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496 </div>
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497 </body>
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498 </html>