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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
author bgruening
date Wed, 07 Feb 2018 06:22:58 -0500
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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1 <!doctype html>
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2 <html>
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3 <head>
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4 <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title>
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5 <link rel="stylesheet" type="text/css" href="css/bacteria.css">
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6 <meta charset="utf-8">
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7 </head>
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8 <body>
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9 <div id="header">
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10 <div class="top-header">
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11 <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">
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12 <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>
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13 <span class="white">Version <span id="antismash-version">4.0.2</span></span>
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14 </span>
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15 <div id="icons">
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16 <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>
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17 <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a>
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18 <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a>
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19 <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a>
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20 <div id="downloadmenu">
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21 <ul id="downloadoptions">
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22 <li><a href="ARBH01000003.1.zip">Download all results</a></li><li><a href="ARBH01000003.1.geneclusters.xls">Download XLS overview file</a></li><li><a href="ARBH01000003.1.final.embl">Download EMBL summary file</a></li><li><a href="ARBH01000003.1.final.gbk">Download GenBank summary file</a></li></ul>
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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23 </div>
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24 </div>
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25 </div>
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26 <div id="buttons">
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27 <span id="cluster-type">Select Gene Cluster:</span>
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28 <ul id="clusterbuttons">
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29 <li><div class="arrow-left" id="prev-cluster"></div></li>
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30 <li class="clbutton"><a href="#">Overview</a></li>
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31 <li class="clbutton t1pks cluster-1"><a href="#cluster-1">1</a></li><li id="last-clbutton"><div class="arrow-right" id="next-cluster"></div></li>
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32 </ul>
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33 </div>
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34 </div>
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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35
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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36 <!-- overview page -->
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37 <div class="page" id="overview">
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38 <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3>
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39 <table id="cluster-overview">
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40 <thead>
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41 <tr>
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42 <th>Cluster</th>
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43 <th>Type</th>
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44 <th>From</th>
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45 <th>To</th>
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46 <th>Most similar known cluster</th>
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47 <th>MIBiG BGC-ID</th>
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48 </tr>
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49 </thead>
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50 <tbody>
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51 <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="http://antismash.secondarymetabolites.org/help#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
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52 </table>
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53 </div>
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54
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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55 <div class="page" id="cluster-1"><h3>ARBH01000003.1 - Cluster 1 - T1pks</h3><div class="sidepanel"><div class="structure"><h3>Predicted core structure</h3><a href="images/nostructure_icon.png" target="_new"><img src="images/nostructure_icon.png"></a><div class="as-structure-warning">Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account</div></div><div class="more-details"><h3>Prediction details</h3><dl class="prediction-text"><dt>Monomers prediction:</dt><dd>(mal)</dd><dt>ctg1_1</dt><dd>PKS signature: mal<br></dd><dd>Minowa: mal<br></dd><dd>consensus: mal<br></dd></dl></div></div><div class="content"><div class="description-container"><h3>Gene cluster description</h3><div class="cluster-download"><a href="ARBH01000003.1.cluster001.gbk">Download cluster GenBank file</a></div><div class="description-text">ARBH01000003.1 - Gene Cluster 1. Type = t1pks. Location: 1 - 3500 nt. Click on genes for more information.</div><a class="cluster-rules-header" id="cluster-1-rules-header" href="#cluster-1">Show pHMM detection rules used</a><div class="cluster-rules" id="cluster-1-rules">t1pks: ((PKS_KS &amp; PKS_AT) or (ene_KS &amp; PKS_AT) or (mod_KS &amp; PKS_AT) or (hyb_KS &amp; PKS_AT) or (itr_KS &amp; PKS_AT) or (tra_KS &amp; PKS_AT))<br></div><div id="cluster-1-svg"></div></div><div class="legend"><h4>Legend:</h4><div><div><div class="legend-field legend-type-biosynthetic"></div><div class="legend-label">core biosynthetic genes</div></div><div><div class="legend-field legend-type-biosynthetic-additional"></div><div class="legend-label">additional biosynthetic genes</div></div><div><div class="legend-field legend-type-transport"></div><div class="legend-label">transport-related genes</div></div><div><div class="legend-field legend-type-regulatory"></div><div class="legend-label">regulatory genes</div></div><div><div class="legend-field legend-type-other"></div><div class="legend-label">other genes</div></div></div></div><div class="details"><h3>Detailed annotation</h3><div class="details-svg" id="cluster-1-details-svg"></div></div></div></div><div id="footer">
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56 <div id="logos">
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57 <table id="logo-table">
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58 <tr>
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59 <td>
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60 <img src="images/tueblogo.gif">
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61 </td>
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62 <td>
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63 <img src="images/ruglogo.gif">
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64 </td>
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65 <td>
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66 <img src="images/ucsflogo.gif">
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67 </td>
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68 <td>
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69 <img src="images/wur-logo.png">
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70 </td>
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71 </tr>
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72 <tr>
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73 <td>
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74 <img src="images/uomlogo.jpg">
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75 </td>
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76 <td>
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77 <img src="images/dziflogo.png">
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78 </td>
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79 <td>
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80 <img src="images/cfb-logo.png">
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81 </td>
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82 <td>
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83 </td>
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84 </tr>
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85 </table>
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86 </div>
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87 <div id="copyright">
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88 If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>.
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89 </div>
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90 </div>
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91
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92 <script src="js/jquery.js"></script>
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93 <script src="js/purl.js"></script>
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94 <script src="js/d3.v2.js"></script>
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95 <script src="js/svgene.js"></script>
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96 <script src="js/jsdomain.js"></script>
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97 <script src="js/clusterblast.js"></script>
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98 <script src="js/domainalign.js"></script>
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99 <script src="geneclusters.js"></script>
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100 <script type="text/javascript">
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101 function toggle_downloadmenu(event) {
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102 event.preventDefault();
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103 $("#downloadmenu").fadeToggle("fast", "linear");
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104 }
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105
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106 function switch_to_cluster() {
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107 setTimeout(function() {
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108 var url = $.url();
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109 $(".page").hide();
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110 $("li.clbutton").removeClass("active");
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111 var anchor = url.data.attr.fragment;
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112 if (anchor == "") {
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113 anchor = "overview";
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114 }
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115 $("#" + anchor).show();
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116 if (anchor != "overview") {
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117 $("li.clbutton." + anchor).addClass("active");
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118 }
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119
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120 if (geneclusters[anchor] !== undefined) {
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121 svgene.drawClusters(anchor+"-svg", [geneclusters[anchor]], 20, 700);
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122 }
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123 if ($("#" + anchor + "-details-svg").length > 0) {
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124 jsdomain.drawDomains(anchor+ "-details-svg", details_data[anchor], 40, 700);
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125 }
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126 $("#" + anchor + " .clusterblast-selector").change();
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127 $("#" + anchor + " .domainalign-selector").change();
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128 }, 1);
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129 }
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130
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131 function next_cluster() {
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132 var num_clusters = Object.keys(geneclusters).length;
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133 var url = $.url();
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134 var anchor = url.data.attr.fragment;
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135 var href = "#" + anchor;
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136 if (anchor == "" || anchor == "overview") {
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137 anchor = "cluster-0";
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138 }
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139 var cluster_number = parseInt(anchor.split('-')[1]);
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140 var next_cluster_number = cluster_number + 1;
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141 if (next_cluster_number <= num_clusters) {
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142 href = "#cluster-" + next_cluster_number;
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143 } else {
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144 href = "#overview";
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145 }
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146 window.location.href = href;
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147 switch_to_cluster();
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148 }
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149
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150 function previous_cluster() {
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151 var num_clusters = Object.keys(geneclusters).length;
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152 var url = $.url();
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153 var anchor = url.data.attr.fragment;
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154 var href = "#" + anchor;
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155 if (anchor == "" || anchor == "overview") {
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156 anchor = "cluster-0";
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157 }
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158 var cluster_number = parseInt(anchor.split('-')[1]);
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159 var prev_cluster_number = cluster_number - 1;
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160 if (prev_cluster_number == 0 ) {
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161 href = "#overview";
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162 } else if (prev_cluster_number < 0){
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163 href = "#cluster-" + num_clusters;
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164 } else {
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165 href = "#cluster-" + prev_cluster_number;
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166 }
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167 window.location.href = href;
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168 switch_to_cluster();
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169 }
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170
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171 function toggle_cluster_rules(ev) {
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172 ev.preventDefault();
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173 var id = $(this).attr('id').replace(/-header/, '');
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174 var rules = $('#' + id);
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175 if (rules.css('display') == "none") {
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176 $(this).text('Hide pHMM detection rules used');
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177 } else {
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178 $(this).text('Show pHMM detection rules used');
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179 }
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180 rules.fadeToggle("fast", "linear");
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181 }
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182
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183 function map_type_to_desc(type) {
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184 switch(type) {
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185 case "nrps": return "NRPS";
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186 case "t1pks": return "Type I PKS";
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187 case "t2pks": return "Type II PKS";
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188 case "t3pks": return "Type III PKS";
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189 case "t4pks": return "Type IV PKS";
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190 default: return type;
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191 }
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192 }
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193
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194 function copyToClipboard (text) {
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195 window.prompt ("Copy to clipboard: Ctrl+C, Enter", text);
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196 }
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197
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198 $(document).ready(function() {
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199
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200 $("#download").click(toggle_downloadmenu);
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201
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202 $("#next-cluster").click(next_cluster);
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203 $("#prev-cluster").click(previous_cluster);
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204
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205 $(".clbutton").click(function() {
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206 /* Make sure that even if user missed the link and clicked the
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207 background we still have the correct anchor */
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208 var href = $(this).children().first().attr('href');
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209
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210 if (href === undefined) {
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211 return;
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212 }
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213 window.location.href = href;
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214
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215 switch_to_cluster();
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216 }).mouseover(function() {
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217 /* Set the select cluster label text to cluster type */
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218 var classes = $(this).attr('class').split(' ');
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219 if (classes.length < 2) {
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220 return;
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221 }
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222 if (classes[1] == 'separator') {
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223 return;
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224 }
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225 var cluster_type = map_type_to_desc(classes[1]);
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226 var label = $('#cluster-type');
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227 label.data("orig_text", label.text());
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228 label.text(cluster_type + ":");
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229 }).mouseout(function() {
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230 /* and reset the select cluster label text */
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231 var label = $('#cluster-type');
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232 label.text(label.data("orig_text"));
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233 });
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234
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235 $('.clusterblast-selector').change(function() {
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236 var id = $(this).attr('id').replace('-select', '');
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237 var url = $(this).val();
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238 $.get(url, function(data) {
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239 $('#' + id + '-svg').html(data);
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240 clusterblast.init(id + '-svg');
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241 // id =
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242 }, 'html');
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243 $('#' + id + '-download').off('click');
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244 $('#' + id + '-download').click(function () {
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245 var url = $("#" + id + "-select").val();
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246 window.open(url, '_blank');
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247 });
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248 });
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249
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250 $('.domainalign-selector').change(function() {
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251 var id = $(this).attr('id').replace('-select', '');
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252 var url = $(this).val();
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253 $.get(url, function(data) {
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254 $('#' + id + '-svg').html(data);
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255 domainalign.init(id + '-svg');
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256 // id =
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257 }, 'html');
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258 $('#' + id + '-download').off('click');
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259 $('#' + id + '-download').click(function () {
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260 var url = $("#" + id + "-select").val();
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261 window.open(url, '_blank');
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262 });
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263 });
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264
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265 $('.cluster-rules-header').click(toggle_cluster_rules);
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266
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267 switch_to_cluster();
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268
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269 });
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270 </script>
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271
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272 </body>
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273 </html>