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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
author bgruening
date Tue, 05 Jul 2022 10:37:38 +0000
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4:e78e25d3b4bd 5:bc88856eddab
1
2 <!doctype html>
3 <html lang="en">
4 <head>
5 <meta charset="utf-8" />
6 <title>input_tempfile - 1 region(s) - antiSMASH results</title>
7 <style>img {width: 20px; height: 20px;}</style>
8 <link rel="stylesheet" type="text/css" href="css/bacteria.css">
9 <meta property="og:title" content="input_tempfile - 1 record(s) - 1 region(s)" />
10 <meta property="og:description" content="">
11 <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/bacteria_logo.png" />
12 <meta property="og:image:alt" content="antiSMASH logo" />
13 <meta property="og:image:width" content="600" />
14 <meta property="og:image:height" content="600" />
15 <meta property="og:url" content="https://antismash.secondarymetabolites.org/upload/input_tempfile/index.html" />
16 <meta property="og:type" content="website" />
17 <meta name="twitter:card" content="summary" />
18 <meta name="twitter:site" content="@antismash_dev" />
19 </head>
20
21 <body>
22 <div id="header">
23 <nav>
24 <div class="main-link">
25 <div>
26 <a href="https://antismash.secondarymetabolites.org/">
27 <img src="images/bacteria_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;">
28 </a>
29 </div>
30 <div>
31 <a href="https://antismash.secondarymetabolites.org/">
32 antiSMASH version 6.1.1
33 </a>
34 </div>
35 </div>
36 <div class="custom-description"></div>
37 <div class="ancillary-links">
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>
39 <ul class="dropdown-options">
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
45 </ul>
46 </div>
47 <div class="ancillary-link"><a href="https://antismash.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://antismash.secondarymetabolites.org/#!/contact"><img src="images/contact.svg" alt="contact"> &nbsp; Contact</a></div>
50 </div>
51 </nav>
52 <div id="buttons">
53 <span id="region-type">Select genomic region:</span>
54 <div id="regionbuttons">
55 <div class="arrow-left" id="prev-region"></div>
56 <div class="regbutton" style="min-width: inherit;"><a href="#">Overview</a></div>
57 <div style="display: flex; flex-wrap: wrap">
58
59
60 <div class="regbutton PKS T1PKS r1c1">
61 <a href="#r1c1">1.1</a>
62 </div>
63
64
65 </div>
66 <div id="last-regbutton"><div class="arrow-right" id="next-region"></div></div>
67 </div>
68 </div>
69 </div>
70
71 <!-- overview page -->
72
73 <div class="page" id="overview">
74
75
76 <h3>Identified secondary metabolite regions using strictness &#39;relaxed&#39;<span id="truncated"></span></h3>
77
78 <div class="overview-layout">
79 <div id="record-tables">
80 <div id="single-record-tables">
81 <div class="record-overview-header">
82 <strong>ARBH01000003.1</strong>
83 <div class="download-container">
84 <div class="download-icon-inverse download-svg" data-tag="record-minimap-1" data-filename="ARBH01000003.1_overview.svg">
85 </div>
86 </div>
87 </div>
88 <div class="record-overview-details">
89 <svg id="record-minimap-1" class="record-overview-svg" height="1" width="1"></svg>
90 <table class="region-table">
91 <thead>
92 <tr>
93 <th>Region</th>
94 <th>Type</th>
95 <th>From</th>
96 <th>To</th>
97 <th colspan="2">Most similar known cluster</th>
98 <th>Similarity</th>
99 </tr>
100 </thead>
101 <tbody>
102 <tr class="linked-row odd" data-anchor="#r1c1">
103 <td class="regbutton PKS T1PKS r1c1">
104 <a href="#r1c1">Region&nbsp1</a>
105 </td>
106 <td>
107
108 <a class="external-link" href="https://docs.antismash.secondarymetabolites.org/glossary/#t1pks" target="_blank">T1PKS</a>
109 </td>
110 <td class="digits">1</td>
111 <td class="digits table-split-left">3,500</td>
112
113 <td colspan="3"></td>
114
115 </tr>
116
117 </tbody>
118 </table>
119 </div>
120 </div>
121
122
123 </div>
124
125 </div>
126 </div>
127
128
129
130
131
132
133
134 <div class="page" id='r1c1' style="display: none;">
135 <div class="region-grid">
136 <div class = "content">
137 <div class ="description-container">
138 <div class="heading"> ARBH01000003.1 - Region 1 - T1PKS <div class="help-container"> <div class="help-icon" data-id="region_svg-help-5"></div> <span class="help-tooltip" id="region_svg-help-5">Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.<br>More detailed help is available <a class='external-link' href='https://docs.antismash.secondarymetabolites.org/understanding_output/#the-antismash-5-region-concept' target='_blank'>here</a>.</span></div></div>
139 <div class="region-download">
140 <a href = ARBH01000003.1.region001.gbk>Download region GenBank file</a>
141 </div>
142 <div class="region-download">
143 <div class="link-like download-svg" data-tag="r1c1-svg" data-filename="ARBH01000003.1_r1c1.svg">Download region SVG</div>
144 </div>
145 <div class = 'description-text'>
146 Location: 1 - 3,500 nt. (total: 3,500 nt)
147
148 <a class="cluster-rules-header" id="r1c1-rules-header" href="#r1c1">Show pHMM detection rules used</a>
149
150
151 <div class="contig-edge-warning">Region on contig edge.</div>
152
153 </div>
154
155 <div class="cluster-rules" id="r1c1-rules">T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))</div>
156
157 <div class="region-svg-container">
158 <div id='r1c1-svg'>
159 </div>
160 </div>
161 </div>
162 <div class="legend">
163 <h4>Legend:</h4>
164 <div class="legend-items">
165 <div class="button-like legend-selector" data-id="legend-type-biosynthetic">
166 <div class="legend-field legend-type-biosynthetic"></div>
167 <div class="legend-label">core biosynthetic genes</div>
168 </div>
169 <div class="button-like legend-selector" data-id="legend-type-biosynthetic-additional">
170 <div class="legend-field legend-type-biosynthetic-additional"></div>
171 <div class="legend-label">additional biosynthetic genes</div>
172 </div>
173 <div class="button-like legend-selector" data-id="legend-type-transport">
174 <div class="legend-field legend-type-transport"></div>
175 <div class="legend-label">transport-related genes</div>
176 </div>
177 <div class="button-like legend-selector" data-id="legend-type-regulatory">
178 <div class="legend-field legend-type-regulatory"></div>
179 <div class="legend-label">regulatory genes</div>
180 </div>
181 <div class="button-like legend-selector" data-id="legend-type-other">
182 <div class="legend-field legend-type-other"></div>
183 <div class="legend-label">other genes</div>
184 </div>
185 <div style="margin-right: 2em;"></div>
186 <div class="button-like legend-selector" data-id="legend-resistance">
187 <div class="legend-symbol">
188 <svg viewbox="0 0 8 8">
189 <rect x=0 y=2 height=4 width=8 class="svgene-resistance"></rect>
190 </svg>
191 </div>
192 <div class="legend-label">resistance</div>
193 </div>
194
195 <div class="button-like legend-selector" data-id="legend-tta-codon">
196 <div class="legend-symbol">
197 <svg viewbox="0 0 6 6">
198 <polyline class="svgene-tta-codon" points="3,0 0,6 6,6 3,0"></rect>
199 </svg>
200 </div>
201 <div class="legend-label">TTA codons</div>
202 </div>
203
204
205 </div>
206 </div>
207 <div class="zoom-buttons">
208 <div class="button-like zoom-button zoom-reset"><img src="images/expand-arrows-alt-solid.svg" alt="reset zoom">reset view</div>
209 <div class="button-like zoom-button zoom-in"><img src="images/search-solid.svg" alt="zoom">zoom to selection</div>
210 </div>
211 </div>
212
213 <div class="focus-panel">
214 <div class="heading">
215 <span>Gene details</span>
216 <div class="help-container"> <div class="help-icon" data-id="focus-panel-help-6"></div> <span class="help-tooltip" id="focus-panel-help-6">Shows details of the most recently selected gene, including names, products, location, and other annotations.</span></div>
217 </div>
218 <div class="focus-panel-content focus-panel-content-r1c1">
219 <div style="text-align: center; margin-top: 30%;">
220 Select a gene to view the details available for it
221 </div>
222 </div>
223 </div>
224
225
226 <div class="body-details">
227 <div class="body-details-headers">
228
229
230 <div class="body-details-header r1c1-hAMRonize" data-name="r1c1-hAMRonize">
231 hAMRonize
232 </div>
233
234
235
236 <div class="body-details-header r1c1-nrps_pks" data-name="r1c1-nrps_pks">
237 NRPS/PKS domains
238 </div>
239
240
241
242 <div class="body-details-header r1c1-knownclusterblast" data-name="r1c1-knownclusterblast">
243 KnownClusterBlast
244 </div>
245
246 <div class="body-details-header r1c1-subclusterblast" data-name="r1c1-subclusterblast">
247 SubClusterBlast
248 </div>
249
250
251
252
253 </div>
254
255
256 <div class="body-details-section r1c1-hAMRonize">
257 <div class="more-details">
258 <div class="heading">
259 <span>External annotation</span>
260 <div class="help-container"> <div class="help-icon" data-id="general_details-help-1"></div> <span class="help-tooltip" id="general_details-help-1">This annotation was made externally by 'hAMRonize' and not by antiSMASH</span></div>
261 </div>
262 <div class="prediction-text" style="padding-left:2em;padding-top:2em;">
263 <table><thead></thead>
264 <tbody>
265 <tr><td>Name</td><td>&nbsp;</td><td><strong>hAMRonize</strong></td></tr>
266
267 <tr><td>Version</td><td>&nbsp;</td><td>?</td></tr>
268
269
270 <tr><td>Description</td><td>&nbsp;</td><td>Tool for combining results</td></tr>
271
272 </tbody>
273 </table>
274
275
276 Configuration:
277 <div class="collapser collapser-target-sideloader-tool collapser-level-none"> </div><div class="collapser-content">
278 <table>
279 <thead>
280 <tr><th>Setting</th><th></th><th>Value</th></tr>
281 </thead>
282 <tbody>
283 <tr><td>multisetting</td><td>&nbsp;</td><td>first, second</td></tr><tr><td>verbose</td><td>&nbsp;</td><td>true</td></tr>
284 </tbody>
285 </table>
286 </div>
287
288 </div>
289 <div class="prediction-text" style="padding-left:2em;padding-top:2em;">
290 <table>
291 <thead></thead>
292 <tbody>
293 <tr><td>Type</td><td>&nbsp;</td><td>Subregion</td></tr>
294 <tr><td>Location</td><td>&nbsp;</td><td>2 - 3,501</td></tr>
295 <tr><td>Label</td><td>&nbsp;</td><td>mecA</td></tr>
296 </tbody>
297 </table>
298
299 Additional area details:
300 <div class="collapser collapser-target-sideloader-detail collapser-level-all expanded"> </div><div class="collapser-content" style="display:block;">
301 <table>
302 <thead>
303 <tr><th>Name</th><th></th><th>Value</th></tr>
304 </thead>
305 <tbody>
306 <tr><td>score</td><td>&nbsp;</td><td>100</td></tr>
307 </tbody>
308 </table>
309 </div>
310
311 </div><div class="prediction-text" style="padding-left:2em;padding-top:2em;">
312 <table>
313 <thead></thead>
314 <tbody>
315 <tr><td>Type</td><td>&nbsp;</td><td>Subregion</td></tr>
316 <tr><td>Location</td><td>&nbsp;</td><td>2 - 3,501</td></tr>
317 <tr><td>Label</td><td>&nbsp;</td><td>mecA</td></tr>
318 </tbody>
319 </table>
320
321 Additional area details:
322 <div class="collapser collapser-target-sideloader-detail collapser-level-all expanded"> </div><div class="collapser-content" style="display:block;">
323 <table>
324 <thead>
325 <tr><th>Name</th><th></th><th>Value</th></tr>
326 </thead>
327 <tbody>
328 <tr><td>score</td><td>&nbsp;</td><td>100</td></tr>
329 </tbody>
330 </table>
331 </div>
332
333 </div>
334 </div>
335 </div>
336
337
338
339 <div class="body-details-section r1c1-nrps_pks">
340 <div class="details">
341 <div class="heading">
342 <span>Detailed domain annotation</span>
343 <div class="help-container"> <div class="help-icon" data-id="nrps-domain-help-2"></div> <span class="help-tooltip" id="nrps-domain-help-2">Shows <a href='https://docs.antismash.secondarymetabolites.org/glossary/#nrps' target='_blank'>NRPS</a>- and <a href='https://docs.antismash.secondarymetabolites.org/glossary/#pks' target='_blank'>PKS</a>-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.<br>A glossary is available <a href='https://docs.antismash.secondarymetabolites.org/modules/nrps_pks_domains/' target='_blank'>here</a>.</span></div>
344 <div class="download-container">
345 <div class="download-icon download-svg" data-tag="r1c1-details-svg" data-filename="ARBH01000003.1_r1c1_nrps_pks.svg">
346 </div>
347 </div>
348 </div>
349 <div class="nrps-pks-domain-buttons">
350 <div class="domains-selected-only switch-container"><span class="switch-desc">Selected features only</span> <label class="switch"> <input class="domains-selected-only" type="checkbox"> <span class="slider"></span> </label></div>
351 <div class="show-module-domains switch-container"><span class="switch-desc">Show module domains</span> <label class="switch"> <input class="show-module-domains" type="checkbox"> <span class="slider"></span> </label></div>
352 </div>
353 <div class="details-svg" id="r1c1-details-svg"></div>
354 </div>
355 </div>
356
357
358
359 <div class="body-details-section r1c1-knownclusterblast">
360 <div class = "knownclusterblast">
361 <div class="heading">
362 <span>Similar known gene clusters</span>
363 <div class="help-container"> <div class="help-icon" data-id="cb-known-help-3"></div> <span class="help-tooltip" id="cb-known-help-3">Shows clusters from the MiBIG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.<br>Click on reference genes to show details of similarities to genes within the current region.<br>Click on an accession to open that entry in the MiBIG database.</span></div>
364 </div>
365
366 <div>
367 <p>No matches found.</p>
368 </div>
369
370 </div>
371 </div>
372
373 <div class="body-details-section r1c1-subclusterblast">
374 <div class = "subclusterblast">
375 <div class="heading">
376 <span>Similar subclusters</span>
377 <div class="help-container"> <div class="help-icon" data-id="cb-sub-help-4"></div> <span class="help-tooltip" id="cb-sub-help-4">Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.<br>Click on reference genes to show details of similarities to genes within the current region.</span></div>
378 </div>
379
380 <div>
381 <p>No matches found.</p>
382 </div>
383
384 </div>
385 </div>
386
387
388
389
390 </div>
391
392 <div class="sidepanel">
393 <div class="sidepanel-details-headers">
394
395
396
397
398
399
400
401
402
403 </div>
404
405
406
407
408
409
410
411
412
413 </div>
414
415 </div>
416
417 </div>
418
419
420 <footer class="footer">
421 <div class="container">
422 <div>
423 <img src="images/bacteria_antismash_logo.svg" style="height:90px;width:unset;">
424 </div>
425 <div class="cite-me">
426 If you have found antiSMASH useful, please <a href="https://antismash.secondarymetabolites.org/#!/about">cite us</a>.
427 </div>
428 <div>
429 <img src="images/bacteria_antismash_icon.svg" style="height:100px;width:unset;">
430 </div>
431 </div>
432 </footer>
433
434 <script src="js/jquery.js"></script>
435 <script src="js/antismash.js"></script>
436 <script src="regions.js"></script>
437 <script>
438 $(document).ready(function() {
439 viewer["start"](all_regions, details_data, resultsData, recordData);
440 })
441 </script>
442
443 <svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink">
444 <defs>
445 <filter id="inset-shadow">
446 <feOffset dx="-2" dy="-2"></feOffset>
447 <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur>
448 <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite>
449 <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood>
450 <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite>
451 <feComponentTransfer in="shadow" result="shadow">
452 <feFuncA type="linear" slope=".95"></feFuncA>
453 </feComponentTransfer>
454 <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite>
455 </filter>
456 </defs>
457 </svg>
458 </body>
459 </html>