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comparison test-data/index.2.html @ 3:5784e268efca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
author bgruening
date Sun, 09 Aug 2020 10:15:12 -0400
parents 593bb8f5488b
children e78e25d3b4bd
comparison
equal deleted inserted replaced
2:3f0077c88c16 3:5784e268efca
1
1 <!doctype html> 2 <!doctype html>
2 <html> 3 <html lang="en">
3 <head> 4 <head>
4 <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title> 5 <meta charset="utf-8" />
5 <link rel="stylesheet" type="text/css" href="css/bacteria.css"> 6 <title>input_tempfile - 0 region(s) - antiSMASH results</title>
6 <meta charset="utf-8"> 7 <style>img {width: 20px; height: 20px;}</style>
7 </head> 8 <link rel="stylesheet" type="text/css" href="css/fungi.css">
8 <body> 9 <meta property="og:title" content="input_tempfile - 0 record(s) - 0 region(s)" />
9 <div id="header"> 10 <meta property="og:description" content="">
10 <div class="top-header"> 11 <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/fungi_logo.png" />
11 <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH"> 12 <meta property="og:image:alt" content="antiSMASH logo" />
12 <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br> 13 <meta property="og:image:width" content="600" />
13 <span class="white">Version <span id="antismash-version">4.0.2</span></span> 14 <meta property="og:image:height" content="600" />
14 </span> 15 <meta property="og:url" content="https://fungismash.secondarymetabolites.org/upload/input_tempfile/index.html" />
15 <div id="icons"> 16 <meta property="og:type" content="website" />
16 <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a> 17 <meta name="twitter:card" content="summary" />
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> 18 <meta name="twitter:site" content="@antismash_dev" />
18 <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a> 19 </head>
19 <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a> 20
20 <div id="downloadmenu"> 21 <body>
21 <ul id="downloadoptions"> 22 <div id="header">
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> 23 <nav>
23 </div> 24 <div class="main-link">
24 </div> 25 <div>
26 <a href="https://fungismash.secondarymetabolites.org/">
27 <img src="images/fungi_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;">
28 </a>
29 </div>
30 <div>
31 <a href="https://fungismash.secondarymetabolites.org/">
32 antiSMASH version 5.1.2
33 </a>
25 </div> 34 </div>
26 <div id="buttons"> 35 </div>
27 <span id="cluster-type">Select Gene Cluster:</span> 36 <div class="custom-description"></div>
28 <ul id="clusterbuttons"> 37 <div class="ancillary-links">
29 <li><div class="arrow-left" id="prev-cluster"></div></li> 38 <div class="ancillary-link dropdown-menu" id="download-dropdown"><a href="#" id="download-dropdown-link"><img src="images/download.svg" alt="download"> &nbsp; Download</a>
30 <li class="clbutton"><a href="#">Overview</a></li> 39 <ul class="dropdown-options">
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> 40
41 <li><a href="input_tempfile.zip">Download all results</a></li>
42
43 <li><a href="input_tempfile.gbk">Download GenBank summary file</a></li>
44
32 </ul> 45 </ul>
33 </div> 46 </div>
47 <div class="ancillary-link"><a href="https://fungismash.secondarymetabolites.org/#!/about"><img src="images/about.svg" alt="about"> &nbsp; About</a></div>
48 <div class="ancillary-link"><a href="https://docs.antismash.secondarymetabolites.org/"><img src="images/help.svg" alt="help"> &nbsp; Help</a></div>
49 <div class="ancillary-link"><a href="https://fungismash.secondarymetabolites.org/#!/contact"><img src="images/contact.svg" alt="contact"> &nbsp; Contact</a></div>
34 </div> 50 </div>
35 51 </nav>
36 <!-- overview page --> 52 <div id="buttons">
37 <div class="page" id="overview"> 53 <span id="region-type">Select genomic region:</span>
38 <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3> 54 <div id="regionbuttons">
39 <table id="cluster-overview"> 55 <div class="arrow-left" id="prev-region"></div>
40 <thead> 56 <div class="regbutton" style="min-width: inherit;"><a href="#">Overview</a></div>
41 <tr> 57 <div style="display: flex; flex-wrap: wrap">
42 <th>Cluster</th> 58
43 <th>Type</th> 59 </div>
44 <th>From</th> 60 <div id="last-regbutton"><div class="arrow-right" id="next-region"></div></div>
45 <th>To</th>
46 <th>Most similar known cluster</th>
47 <th>MIBiG BGC-ID</th>
48 </tr>
49 </thead>
50 <tbody>
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>
52 </table>
53 </div>
54
55 <div class="page" id="cluster-1"><h3>ARBH01000003 - 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 - 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">
56 <div id="logos">
57 <table id="logo-table">
58 <tr>
59 <td>
60 <img src="images/tueblogo.gif">
61 </td>
62 <td>
63 <img src="images/ruglogo.gif">
64 </td>
65 <td>
66 <img src="images/ucsflogo.gif">
67 </td>
68 <td>
69 <img src="images/wur-logo.png">
70 </td>
71 </tr>
72 <tr>
73 <td>
74 <img src="images/uomlogo.jpg">
75 </td>
76 <td>
77 <img src="images/dziflogo.png">
78 </td>
79 <td>
80 <img src="images/cfb-logo.png">
81 </td>
82 <td>
83 </td>
84 </tr>
85 </table>
86 </div>
87 <div id="copyright">
88 If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>.
89 </div> 61 </div>
90 </div> 62 </div>
63 </div>
91 64
92 <script src="js/jquery.js"></script> 65 <!-- overview page -->
93 <script src="js/purl.js"></script> 66
94 <script src="js/d3.v2.js"></script> 67 <div class="page" id="overview">
95 <script src="js/svgene.js"></script> 68 <div class="no-results">No results found on input.</div>
96 <script src="js/jsdomain.js"></script> 69 </div>
97 <script src="js/clusterblast.js"></script> 70
98 <script src="js/domainalign.js"></script>
99 <script src="geneclusters.js"></script>
100 <script type="text/javascript">
101 function toggle_downloadmenu(event) {
102 event.preventDefault();
103 $("#downloadmenu").fadeToggle("fast", "linear");
104 }
105 71
106 function switch_to_cluster() {
107 setTimeout(function() {
108 var url = $.url();
109 $(".page").hide();
110 $("li.clbutton").removeClass("active");
111 var anchor = url.data.attr.fragment;
112 if (anchor == "") {
113 anchor = "overview";
114 }
115 $("#" + anchor).show();
116 if (anchor != "overview") {
117 $("li.clbutton." + anchor).addClass("active");
118 }
119 72
120 if (geneclusters[anchor] !== undefined) {
121 svgene.drawClusters(anchor+"-svg", [geneclusters[anchor]], 20, 700);
122 }
123 if ($("#" + anchor + "-details-svg").length > 0) {
124 jsdomain.drawDomains(anchor+ "-details-svg", details_data[anchor], 40, 700);
125 }
126 $("#" + anchor + " .clusterblast-selector").change();
127 $("#" + anchor + " .domainalign-selector").change();
128 }, 1);
129 }
130 73
131 function next_cluster() {
132 var num_clusters = Object.keys(geneclusters).length;
133 var url = $.url();
134 var anchor = url.data.attr.fragment;
135 var href = "#" + anchor;
136 if (anchor == "" || anchor == "overview") {
137 anchor = "cluster-0";
138 }
139 var cluster_number = parseInt(anchor.split('-')[1]);
140 var next_cluster_number = cluster_number + 1;
141 if (next_cluster_number <= num_clusters) {
142 href = "#cluster-" + next_cluster_number;
143 } else {
144 href = "#overview";
145 }
146 window.location.href = href;
147 switch_to_cluster();
148 }
149 74
150 function previous_cluster() { 75 <footer class="footer">
151 var num_clusters = Object.keys(geneclusters).length; 76 <div class="container">
152 var url = $.url(); 77 <div>
153 var anchor = url.data.attr.fragment; 78 <img src="images/fungi_antismash_logo.svg" style="height:90px;width:unset;">
154 var href = "#" + anchor; 79 </div>
155 if (anchor == "" || anchor == "overview") { 80 <div class="cite-me">
156 anchor = "cluster-0"; 81 If you have found antiSMASH useful, please <a href="https://fungismash.secondarymetabolites.org/#!/about">cite us</a>.
157 } 82 </div>
158 var cluster_number = parseInt(anchor.split('-')[1]); 83 <div>
159 var prev_cluster_number = cluster_number - 1; 84 <img src="images/fungi_antismash_icon.svg" style="height:100px;width:unset;">
160 if (prev_cluster_number == 0 ) { 85 </div>
161 href = "#overview"; 86 </div>
162 } else if (prev_cluster_number < 0){ 87 </footer>
163 href = "#cluster-" + num_clusters;
164 } else {
165 href = "#cluster-" + prev_cluster_number;
166 }
167 window.location.href = href;
168 switch_to_cluster();
169 }
170 88
171 function toggle_cluster_rules(ev) { 89 <script src="js/jquery.js"></script>
172 ev.preventDefault(); 90 <script src="js/antismash.js"></script>
173 var id = $(this).attr('id').replace(/-header/, ''); 91 <script src="regions.js"></script>
174 var rules = $('#' + id); 92 <script>
175 if (rules.css('display') == "none") { 93 $(document).ready(function() {
176 $(this).text('Hide pHMM detection rules used'); 94 viewer["start"](all_regions, details_data, recordData);
177 } else { 95 })
178 $(this).text('Show pHMM detection rules used'); 96 </script>
179 }
180 rules.fadeToggle("fast", "linear");
181 }
182 97
183 function map_type_to_desc(type) { 98 <svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink">
184 switch(type) { 99 <defs>
185 case "nrps": return "NRPS"; 100 <filter id="inset-shadow">
186 case "t1pks": return "Type I PKS"; 101 <feOffset dx="-2" dy="-2"></feOffset>
187 case "t2pks": return "Type II PKS"; 102 <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur>
188 case "t3pks": return "Type III PKS"; 103 <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite>
189 case "t4pks": return "Type IV PKS"; 104 <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood>
190 default: return type; 105 <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite>
191 } 106 <feComponentTransfer in="shadow" result="shadow">
192 } 107 <feFuncA type="linear" slope=".95"></feFuncA>
193 108 </feComponentTransfer>
194 function copyToClipboard (text) { 109 <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite>
195 window.prompt ("Copy to clipboard: Ctrl+C, Enter", text); 110 </filter>
196 } 111 </defs>
197 112 </svg>
198 $(document).ready(function() { 113 </body>
199
200 $("#download").click(toggle_downloadmenu);
201
202 $("#next-cluster").click(next_cluster);
203 $("#prev-cluster").click(previous_cluster);
204
205 $(".clbutton").click(function() {
206 /* Make sure that even if user missed the link and clicked the
207 background we still have the correct anchor */
208 var href = $(this).children().first().attr('href');
209
210 if (href === undefined) {
211 return;
212 }
213 window.location.href = href;
214
215 switch_to_cluster();
216 }).mouseover(function() {
217 /* Set the select cluster label text to cluster type */
218 var classes = $(this).attr('class').split(' ');
219 if (classes.length < 2) {
220 return;
221 }
222 if (classes[1] == 'separator') {
223 return;
224 }
225 var cluster_type = map_type_to_desc(classes[1]);
226 var label = $('#cluster-type');
227 label.data("orig_text", label.text());
228 label.text(cluster_type + ":");
229 }).mouseout(function() {
230 /* and reset the select cluster label text */
231 var label = $('#cluster-type');
232 label.text(label.data("orig_text"));
233 });
234
235 $('.clusterblast-selector').change(function() {
236 var id = $(this).attr('id').replace('-select', '');
237 var url = $(this).val();
238 $.get(url, function(data) {
239 $('#' + id + '-svg').html(data);
240 clusterblast.init(id + '-svg');
241 // id =
242 }, 'html');
243 $('#' + id + '-download').off('click');
244 $('#' + id + '-download').click(function () {
245 var url = $("#" + id + "-select").val();
246 window.open(url, '_blank');
247 });
248 });
249
250 $('.domainalign-selector').change(function() {
251 var id = $(this).attr('id').replace('-select', '');
252 var url = $(this).val();
253 $.get(url, function(data) {
254 $('#' + id + '-svg').html(data);
255 domainalign.init(id + '-svg');
256 // id =
257 }, 'html');
258 $('#' + id + '-download').off('click');
259 $('#' + id + '-download').click(function () {
260 var url = $("#" + id + "-select").val();
261 window.open(url, '_blank');
262 });
263 });
264
265 $('.cluster-rules-header').click(toggle_cluster_rules);
266
267 switch_to_cluster();
268
269 });
270 </script>
271
272 </body>
273 </html> 114 </html>