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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 |
| parents | |
| children | 5784e268efca |
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<!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> <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 & 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>. </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); } 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(); } 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; 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")); }); $('.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> </html>