Mercurial > repos > bgruening > antismash
diff test-data/index.2.html @ 3:5784e268efca draft
"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 |
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--- a/test-data/index.2.html Sat Feb 10 02:37:49 2018 -0500 +++ b/test-data/index.2.html Sun Aug 09 10:15:12 2020 -0400 @@ -1,273 +1,114 @@ -<!doctype html> -<html> - <head> - <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title> - <link rel="stylesheet" type="text/css" href="css/bacteria.css"> - <meta charset="utf-8"> - </head> - <body> - <div id="header"> - <div class="top-header"> - <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH"> - <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics & Secondary Metabolite Analysis SHell</a><br> - <span class="white">Version <span id="antismash-version">4.0.2</span></span> - </span> - <div id="icons"> - <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a> - <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a> - <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a> - <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a> - <div id="downloadmenu"> - <ul id="downloadoptions"> - <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> - </div> - </div> - </div> - <div id="buttons"> - <span id="cluster-type">Select Gene Cluster:</span> - <ul id="clusterbuttons"> - <li><div class="arrow-left" id="prev-cluster"></div></li> - <li class="clbutton"><a href="#">Overview</a></li> - <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> - </ul> - </div> - </div> - <!-- overview page --> - <div class="page" id="overview"> - <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3> - <table id="cluster-overview"> - <thead> - <tr> - <th>Cluster</th> - <th>Type</th> - <th>From</th> - <th>To</th> - <th>Most similar known cluster</th> - <th>MIBiG BGC-ID</th> - </tr> - </thead> - <tbody> - <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> - </table> - </div> +<!doctype html> +<html lang="en"> +<head> + <meta charset="utf-8" /> + <title>input_tempfile - 0 region(s) - antiSMASH results</title> + <style>img {width: 20px; height: 20px;}</style> + <link rel="stylesheet" type="text/css" href="css/fungi.css"> + <meta property="og:title" content="input_tempfile - 0 record(s) - 0 region(s)" /> + <meta property="og:description" content=""> + <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/fungi_logo.png" /> + <meta property="og:image:alt" content="antiSMASH logo" /> + <meta property="og:image:width" content="600" /> + <meta property="og:image:height" content="600" /> + <meta property="og:url" content="https://fungismash.secondarymetabolites.org/upload/input_tempfile/index.html" /> + <meta property="og:type" content="website" /> + <meta name="twitter:card" content="summary" /> + <meta name="twitter:site" content="@antismash_dev" /> +</head> - <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 & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or (tra_KS & 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"> - <div id="logos"> - <table id="logo-table"> - <tr> - <td> - <img src="images/tueblogo.gif"> - </td> - <td> - <img src="images/ruglogo.gif"> - </td> - <td> - <img src="images/ucsflogo.gif"> - </td> - <td> - <img src="images/wur-logo.png"> - </td> - </tr> - <tr> - <td> - <img src="images/uomlogo.jpg"> - </td> - <td> - <img src="images/dziflogo.png"> - </td> - <td> - <img src="images/cfb-logo.png"> - </td> - <td> - </td> - </tr> - </table> - </div> - <div id="copyright"> - If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>. +<body> + <div id="header"> + <nav> + <div class="main-link"> + <div> + <a href="https://fungismash.secondarymetabolites.org/"> + <img src="images/fungi_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;"> + </a> + </div> + <div> + <a href="https://fungismash.secondarymetabolites.org/"> + antiSMASH version 5.1.2 + </a> </div> </div> - - <script src="js/jquery.js"></script> - <script src="js/purl.js"></script> - <script src="js/d3.v2.js"></script> - <script src="js/svgene.js"></script> - <script src="js/jsdomain.js"></script> - <script src="js/clusterblast.js"></script> - <script src="js/domainalign.js"></script> - <script src="geneclusters.js"></script> - <script type="text/javascript"> -function toggle_downloadmenu(event) { - event.preventDefault(); - $("#downloadmenu").fadeToggle("fast", "linear"); -} - -function switch_to_cluster() { - setTimeout(function() { - var url = $.url(); - $(".page").hide(); - $("li.clbutton").removeClass("active"); - var anchor = url.data.attr.fragment; - if (anchor == "") { - anchor = "overview"; - } - $("#" + anchor).show(); - if (anchor != "overview") { - $("li.clbutton." + anchor).addClass("active"); - } - - if (geneclusters[anchor] !== undefined) { - svgene.drawClusters(anchor+"-svg", [geneclusters[anchor]], 20, 700); - } - if ($("#" + anchor + "-details-svg").length > 0) { - jsdomain.drawDomains(anchor+ "-details-svg", details_data[anchor], 40, 700); - } - $("#" + anchor + " .clusterblast-selector").change(); - $("#" + anchor + " .domainalign-selector").change(); - }, 1); -} + <div class="custom-description"></div> + <div class="ancillary-links"> + <div class="ancillary-link dropdown-menu" id="download-dropdown"><a href="#" id="download-dropdown-link"><img src="images/download.svg" alt="download"> Download</a> + <ul class="dropdown-options"> + + <li><a href="input_tempfile.zip">Download all results</a></li> + + <li><a href="input_tempfile.gbk">Download GenBank summary file</a></li> + + </ul> + </div> + <div class="ancillary-link"><a href="https://fungismash.secondarymetabolites.org/#!/about"><img src="images/about.svg" alt="about"> About</a></div> + <div class="ancillary-link"><a href="https://docs.antismash.secondarymetabolites.org/"><img src="images/help.svg" alt="help"> Help</a></div> + <div class="ancillary-link"><a href="https://fungismash.secondarymetabolites.org/#!/contact"><img src="images/contact.svg" alt="contact"> Contact</a></div> + </div> + </nav> + <div id="buttons"> + <span id="region-type">Select genomic region:</span> + <div id="regionbuttons"> + <div class="arrow-left" id="prev-region"></div> + <div class="regbutton" style="min-width: inherit;"><a href="#">Overview</a></div> + <div style="display: flex; flex-wrap: wrap"> + + </div> + <div id="last-regbutton"><div class="arrow-right" id="next-region"></div></div> + </div> + </div> + </div> -function next_cluster() { - var num_clusters = Object.keys(geneclusters).length; - var url = $.url(); - var anchor = url.data.attr.fragment; - var href = "#" + anchor; - if (anchor == "" || anchor == "overview") { - anchor = "cluster-0"; - } - var cluster_number = parseInt(anchor.split('-')[1]); - var next_cluster_number = cluster_number + 1; - if (next_cluster_number <= num_clusters) { - href = "#cluster-" + next_cluster_number; - } else { - href = "#overview"; - } - window.location.href = href; - switch_to_cluster(); -} + <!-- overview page --> + + <div class="page" id="overview"> + <div class="no-results">No results found on input.</div> + </div> + -function previous_cluster() { - var num_clusters = Object.keys(geneclusters).length; - var url = $.url(); - var anchor = url.data.attr.fragment; - var href = "#" + anchor; - if (anchor == "" || anchor == "overview") { - anchor = "cluster-0"; - } - var cluster_number = parseInt(anchor.split('-')[1]); - var prev_cluster_number = cluster_number - 1; - if (prev_cluster_number == 0 ) { - href = "#overview"; - } else if (prev_cluster_number < 0){ - href = "#cluster-" + num_clusters; - } else { - href = "#cluster-" + prev_cluster_number; - } - window.location.href = href; - switch_to_cluster(); -} -function toggle_cluster_rules(ev) { - ev.preventDefault(); - var id = $(this).attr('id').replace(/-header/, ''); - var rules = $('#' + id); - if (rules.css('display') == "none") { - $(this).text('Hide pHMM detection rules used'); - } else { - $(this).text('Show pHMM detection rules used'); - } - rules.fadeToggle("fast", "linear"); -} + -function map_type_to_desc(type) { - switch(type) { - case "nrps": return "NRPS"; - case "t1pks": return "Type I PKS"; - case "t2pks": return "Type II PKS"; - case "t3pks": return "Type III PKS"; - case "t4pks": return "Type IV PKS"; - default: return type; - } -} - -function copyToClipboard (text) { - window.prompt ("Copy to clipboard: Ctrl+C, Enter", text); -} - -$(document).ready(function() { - - $("#download").click(toggle_downloadmenu); - - $("#next-cluster").click(next_cluster); - $("#prev-cluster").click(previous_cluster); - - $(".clbutton").click(function() { - /* Make sure that even if user missed the link and clicked the - background we still have the correct anchor */ - var href = $(this).children().first().attr('href'); - - if (href === undefined) { - return; - } - window.location.href = href; + <footer class="footer"> + <div class="container"> + <div> + <img src="images/fungi_antismash_logo.svg" style="height:90px;width:unset;"> + </div> + <div class="cite-me"> + If you have found antiSMASH useful, please <a href="https://fungismash.secondarymetabolites.org/#!/about">cite us</a>. + </div> + <div> + <img src="images/fungi_antismash_icon.svg" style="height:100px;width:unset;"> + </div> + </div> + </footer> - switch_to_cluster(); - }).mouseover(function() { - /* Set the select cluster label text to cluster type */ - var classes = $(this).attr('class').split(' '); - if (classes.length < 2) { - return; - } - if (classes[1] == 'separator') { - return; - } - var cluster_type = map_type_to_desc(classes[1]); - var label = $('#cluster-type'); - label.data("orig_text", label.text()); - label.text(cluster_type + ":"); - }).mouseout(function() { - /* and reset the select cluster label text */ - var label = $('#cluster-type'); - label.text(label.data("orig_text")); - }); + <script src="js/jquery.js"></script> + <script src="js/antismash.js"></script> + <script src="regions.js"></script> + <script> + $(document).ready(function() { + viewer["start"](all_regions, details_data, recordData); + }) + </script> - $('.clusterblast-selector').change(function() { - var id = $(this).attr('id').replace('-select', ''); - var url = $(this).val(); - $.get(url, function(data) { - $('#' + id + '-svg').html(data); - clusterblast.init(id + '-svg'); - // id = - }, 'html'); - $('#' + id + '-download').off('click'); - $('#' + id + '-download').click(function () { - var url = $("#" + id + "-select").val(); - window.open(url, '_blank'); - }); - }); - - $('.domainalign-selector').change(function() { - var id = $(this).attr('id').replace('-select', ''); - var url = $(this).val(); - $.get(url, function(data) { - $('#' + id + '-svg').html(data); - domainalign.init(id + '-svg'); - // id = - }, 'html'); - $('#' + id + '-download').off('click'); - $('#' + id + '-download').click(function () { - var url = $("#" + id + "-select").val(); - window.open(url, '_blank'); - }); - }); - - $('.cluster-rules-header').click(toggle_cluster_rules); - - switch_to_cluster(); - -}); - </script> - - </body> +<svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink"> + <defs> + <filter id="inset-shadow"> + <feOffset dx="-2" dy="-2"></feOffset> + <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur> + <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite> + <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood> + <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite> + <feComponentTransfer in="shadow" result="shadow"> + <feFuncA type="linear" slope=".95"></feFuncA> + </feComponentTransfer> + <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite> + </filter> + </defs> +</svg> +</body> </html> \ No newline at end of file