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1 <!DOCTYPE HTML>
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16
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17 <html>
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18 <!--base_panels.mako-->
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19
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20
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21
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22 <head>
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23 <title>Galaxy Tool Shed</title>
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24 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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25 <meta name = "viewport" content = "maximum-scale=1.0">
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26 <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
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27
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28 <link href="/static/style/base.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
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29 <link href="/static/style/autocomplete_tagging.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
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30 <link href="/static/style/tool_menu.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
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31
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32
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33 <link href="/static/style/base.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
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34 <link href="/static/style/jquery.rating.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
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35 <style type="text/css">
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36 #center {
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37 right: 0 !important;
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38 }
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39 </style>
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40
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41
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42 <style type="text/css">
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43 body { margin: 0; padding: 0; overflow: hidden; }
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44 #left {
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45 background: #C1C9E5 url(/static/style/menu_bg.png) top repeat-x;
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46 }
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47 .unified-panel-body {
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48 overflow: auto;
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49 }
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50 .toolMenu {
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51 margin-left: 10px;
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52 }
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53 </style>
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54
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55
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56
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57
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58
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59
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60 <script src="/static/scripts/libs/jquery/jquery.js?v=1409176523" type="text/javascript"></script>
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61 <script src="/static/scripts/libs/jquery/jquery.migrate.js?v=1409176523" type="text/javascript"></script>
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62 <script src="/static/scripts/libs/jquery/select2.js?v=1409176523" type="text/javascript"></script>
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63 <script src="/static/scripts/libs/bootstrap.js?v=1409176523" type="text/javascript"></script>
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64 <script src="/static/scripts/libs/underscore.js?v=1409176523" type="text/javascript"></script>
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65 <script src="/static/scripts/libs/backbone/backbone.js?v=1409176523" type="text/javascript"></script>
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66 <script src="/static/scripts/libs/backbone/backbone-relational.js?v=1409176523" type="text/javascript"></script>
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67 <script src="/static/scripts/libs/handlebars.runtime.js?v=1409176523" type="text/javascript"></script>
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68 <script src="/static/scripts/galaxy.base.js?v=1409176523" type="text/javascript"></script>
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69 <script src="/static/scripts/libs/require.js?v=1409176523" type="text/javascript"></script>
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70
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71 <script src="/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1409176523" type="text/javascript"></script>
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72
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73 <script src="/static/scripts/mvc/ui.js?v=1409176523" type="text/javascript"></script>
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74
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75 <script type="text/javascript">
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76 var galaxy_config = {
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77 url: {
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78 styles : "/static/style"
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79 }
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80 };
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81
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82 if (window != window.top)
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83 $('<link href="' + galaxy_config.url.styles + '/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
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84
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85 // console protection
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86 window.console = window.console || {
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87 log : function(){},
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88 debug : function(){},
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89 info : function(){},
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90 warn : function(){},
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91 error : function(){},
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92 assert : function(){}
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93 };
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94
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95 // Set up needed paths.
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96 var galaxy_paths = new GalaxyPaths({
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97 root_path: '/',
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98 image_path: '/static/images',
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99
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100 tool_url: '/api/tools',
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101 history_url: '/api/histories',
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102
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103 datasets_url: '/api/datasets',
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104 sweepster_url: '/visualization/sweepster',
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105 visualization_url: '/visualization/save',
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106 });
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107
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108 require.config({
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109 baseUrl: "/static/scripts",
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110 shim: {
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111 "libs/underscore": { exports: "_" },
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112 "libs/backbone/backbone": { exports: "Backbone" },
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113 "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
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114 }
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115 });
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116
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117 var frame_manager = null;
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118 require(['galaxy.frame'], function(frame) { this.frame_manager = new frame.GalaxyFrameManager(galaxy_config); });
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119 </script>
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120
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121
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122
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123 </head>
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124
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125 <body scroll="no" class="full-content ">
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126 <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;">
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127 <div id="background"></div>
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128 <div id="masthead" class="navbar navbar-fixed-top">
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129 <div class="masthead-inner navbar-inner">
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130
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131
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132 <div style="position: relative; right: -50%; float: left;">
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133 <div style="display: block; position: relative; right: 50%;">
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134
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135 <ul class="nav" border="0" cellspacing="0">
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136
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137
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138
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139
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140
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141 <li class="" style="">
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142 <a class="" data-toggle="dropdown" target="_parent" href="/repository">Repositories</a>
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143 </li>
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144
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145
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146
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147
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148 <li class=" admin-only" style="display: none;">
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149 <a class="" data-toggle="dropdown" target="_parent" href="/admin">Admin</a>
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150 </li>
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151
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152
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153
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154
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155 <li class=" dropdown" style="">
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156 <a class=" dropdown-toggle" data-toggle="dropdown">Help<b class='caret'></b></a>
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157 <ul class="dropdown-menu">
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158 <li>
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159
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160 <a target="_blank" href="http://wiki.g2.bx.psu.edu/Support">Support</a>
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161 </li>
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162 <li>
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163
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164 <a target="_blank" href="http://wiki.g2.bx.psu.edu/Tool%20Shed">Tool shed wiki</a>
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165 </li>
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166 <li>
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167
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168 <a target="_blank" href="http://wiki.g2.bx.psu.edu/">Galaxy wiki</a>
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169 </li>
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170 <li>
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171
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172 <a target="_blank" href="http://galaxycast.org">Video tutorials (screencasts)</a>
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173 </li>
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174 <li>
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175
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176 <a target="_blank" href="http://wiki.g2.bx.psu.edu/Citing%20Galaxy">How to Cite Galaxy</a>
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177 </li>
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178 </ul>
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179 </li>
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180
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181
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182
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183
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184 <li class=" dropdown" style="">
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185 <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a>
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186 <ul class="dropdown-menu">
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187 <li>
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188
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189 <a target="galaxy_main" href="/user/login">Login</a>
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190 </li>
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191 <li>
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192
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193 <a target="galaxy_main" href="/user/create?cntrller=user">Register</a>
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194 </li>
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195 </ul>
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196 </li>
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197
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198
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199 <li class=" dropdown" style="display: none;">
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200 <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a>
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201 <ul class="dropdown-menu">
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202 <li>
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203 <a>Logged in as <span id="user-email"></span></a>
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204 </li>
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205 <li>
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206
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207 <a target="galaxy_main" href="/user?cntrller=user">Preferences</a>
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208 </li>
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209 <li>
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210
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211 <a target="galaxy_main" href="/user/api_keys?cntrller=user">API Keys</a>
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212 </li>
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213 <li>
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214
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215 <a target="_top" href="/user/logout">Logout</a>
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216 </li>
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217 <li class="divider"></li>
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218 </ul>
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219 </li>
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220
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221 </ul>
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222 </div>
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223 </div>
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224
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225 <div class="title">
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226 Galaxy Tool Shed
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227 </a>
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228 </div>
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229
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230 </div>
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231 </div>
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232 <div id="messagebox" class="panel-info-message">
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233 </div>
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234
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235
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236
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237
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238
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239
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240 <div id="overlay" style='display: none;'>
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241
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242 <div id="overlay-background" class="modal-backdrop fade "></div>
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243
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244 <div id="dialog-box" class="modal dialog-box" border="0" style='display: none;'>
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245 <div class="modal-header">
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246 <span><h3 class='title'></h3></span>
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247 </div>
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248 <div class="modal-body"></div>
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249 <div class="modal-footer">
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250 <div class="buttons" style="float: right;"></div>
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251 <div class="extra_buttons" style=""></div>
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252 <div style="clear: both;"></div>
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253 </div>
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254 </div>
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255
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256 </div>
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257
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258 <div id="left">
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259
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260
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261 <div class="unified-panel-header" unselectable="on">
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262 <div class='unified-panel-header-inner'>29 valid tools on Aug 27, 2014</div>
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263 </div>
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264 <div class="unified-panel-body">
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265 <div class="toolMenu">
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266 <div class="toolSectionList">
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267 <div class="toolSectionPad"></div>
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268 <div class="toolSectionTitle">
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269 All Repositories
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270 </div>
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271 <div class="toolTitle">
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272 <a href="/repository">Browse by category</a>
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273 </div>
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274 </div>
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275 </div>
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276 </div>
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277
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278 <div class="unified-panel-footer">
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279 <div class="panel-collapse"></span></div>
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280 <div class="drag"></div>
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281 </div>
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282 </div>
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283 <div id="center">
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284
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285
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286 <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="/repository/view_repository?status=done&message=&id=149c5ffa3420467d"></iframe>
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287
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288 </div>
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289 </div>
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290 </body>
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291
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292 <script src="/static/scripts/libs/jquery/jquery.event.drag.js?v=1409176523" type="text/javascript"></script>
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293 <script src="/static/scripts/libs/jquery/jquery.event.hover.js?v=1409176523" type="text/javascript"></script>
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294 <script src="/static/scripts/libs/jquery/jquery.form.js?v=1409176523" type="text/javascript"></script>
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295 <script src="/static/scripts/libs/jquery/jquery.rating.js?v=1409176523" type="text/javascript"></script>
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296 <script src="/static/scripts/galaxy.panels.js?v=1409176523" type="text/javascript"></script>
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297 <script type="text/javascript">
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298
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299 ensure_dd_helper();
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300
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301 var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } );
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302 force_left_panel = function( x ) { lp.force_panel( x ) };
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303
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304
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305 </script>
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306 <![if !IE]>
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307 <script type="text/javascript">
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308 var upload_form_error = function( msg ) {
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309 if ( ! $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").size() ) {
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310 $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage" name="upload_error">' + msg + '</div><p/>' );
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311 } else {
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312 $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg );
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313 }
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314 }
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315 var uploads_in_progress = 0;
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316 jQuery( function() {
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317 $("iframe#galaxy_main").load( function() {
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318 $(this).contents().find("form").each( function() {
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319 if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){
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320 $(this).submit( function() {
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321 // Only bother using a hidden iframe if there's a file (e.g. big data) upload
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322 var file_upload = false;
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323 $(this).find("input[galaxy-ajax-upload]").each( function() {
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324 if ( $(this).val() != '' ) {
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325 file_upload = true;
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326 }
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327 });
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328 if ( ! file_upload ) {
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329 return true;
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330 }
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331 // Make a synchronous request to create the datasets first
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332 var async_datasets;
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333 var upload_error = false;
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334 $.ajax( {
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335 async: false,
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336 type: "POST",
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337 url: "/tool_runner/upload_async_create",
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338 data: $(this).formSerialize(),
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339 dataType: "json",
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340 success: function(array_obj, status) {
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341 if (array_obj.length > 0) {
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342 if (array_obj[0] == 'error') {
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343 upload_error = true;
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344 upload_form_error(array_obj[1]);
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345 } else {
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346 async_datasets = array_obj.join();
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347 }
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348 } else {
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349 // ( gvk 1/22/10 ) FIXME: this block is never entered, so there may be a bug somewhere
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350 // I've done some debugging like checking to see if array_obj is undefined, but have not
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351 // tracked down the behavior that will result in this block being entered. I believe the
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352 // intent was to have this block entered if the upload button is clicked on the upload
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353 // form but no file was selected.
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354 upload_error = true;
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355 upload_form_error( 'No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch data.' );
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356 }
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357 }
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358 } );
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359 if (upload_error == true) {
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360 return false;
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361 } else {
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362 $(this).find("input[name=async_datasets]").val( async_datasets );
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363 $(this).append("<input type='hidden' name='ajax_upload' value='true'>");
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364 }
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365 // iframe submit is required for nginx (otherwise the encoding is wrong)
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366 $(this).ajaxSubmit( { iframe: true,
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367 complete: function (xhr, stat) {
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368 uploads_in_progress--;
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369 if (uploads_in_progress == 0) {
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370 window.onbeforeunload = null;
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371 }
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372 }
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373 } );
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374 uploads_in_progress++;
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375 window.onbeforeunload = function() { return "Navigating away from the Galaxy analysis interface will interrupt the file upload(s) currently in progress. Do you really want to do this?"; }
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376 if ( $(this).find("input[name='folder_id']").val() != undefined ) {
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377 var library_id = $(this).find("input[name='library_id']").val();
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378 var show_deleted = $(this).find("input[name='show_deleted']").val();
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379 if ( location.pathname.indexOf( 'admin' ) != -1 ) {
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380 $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
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381 } else {
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382 $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
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383 }
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384 } else {
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385 $("iframe#galaxy_main").attr("src","/tool_runner/upload_async_message");
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386 }
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387 return false;
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388 });
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389 }
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390 });
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391 });
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392 });
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393 </script>
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394 <![endif]>
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395
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396 </html>
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