Repository 'antismash'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/antismash

Changeset 3:5784e268efca (2020-08-09)
Previous changeset 2:3f0077c88c16 (2018-02-10) Next changeset 4:e78e25d3b4bd (2022-05-31)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
modified:
antismash.xml
test-data/ARBH01000003.1.cluster001
test-data/index.2.html
test-data/index.html
b
diff -r 3f0077c88c16 -r 5784e268efca antismash.xml
--- a/antismash.xml Sat Feb 10 02:37:49 2018 -0500
+++ b/antismash.xml Sun Aug 09 10:15:12 2020 -0400
[
b'@@ -1,12 +1,14 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool id="antismash" name="Antismash" version="4.1" profile="17.01">\n+<tool id="antismash" name="Antismash" version="5.1.2" profile="17.01">\n     <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>\n     <requirements>\n-        <requirement type="package" version="4.1">antismash</requirement>\n+        <requirement type="package" version="5.1.2">antismash</requirement>\n     </requirements>\n     <version_command>antismash --version</version_command>\n     <command detect_errors="aggressive">\n <![CDATA[\n+        export PYTHONWARNINGS="ignore::FutureWarning" &&\n+\n         #import os, glob\n         #set $htmloutputfolder = $html.files_path\n         #if str($infile.ext) == \'genbank\':\n@@ -18,21 +20,27 @@\n         ln -s \'$infile\' input_tempfile.$file_extension &&\n \n         ## create html folder\n-        mkdir -p $htmloutputfolder &&\n+        mkdir -p \'$htmloutputfolder\' &&\n \n         antismash\n             --cpus "\\${GALAXY_SLOTS:-12}"\n-            --taxon \'${taxon}\'\n-            --input-type \'${input_type}\'\n+            --taxon \'${cond_taxon.taxon}\'\n+\n+            --genefinding-tool $cond_taxon.genefinding_tool\n \n-            ${clusterblast}\n-            ${subclusterblast}\n-            ${smcogs}\n-            ${inclusive}\n-            ${borderpredict}\n-            ${tta}\n+            ${cb_general}\n+            ${cb_subclusters}\n+            ${cb_knownclusters}\n+            ${smcog_trees}\n+            --tta-threshold ${tta_threshold}\n             ${asf}\n-            ${full_hmmer}\n+\n+            ${extra_cluster}\n+            ${clusterhmmer}\n+            ${fullhmmer}\n+            #if $cond_taxon.taxon == \'fungi\':\n+                $cond_taxon.cassis\n+            #end if\n \n             input_tempfile.$file_extension &&\n \n@@ -45,40 +53,61 @@\n     <inputs>\n         <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>\n \n-        <param argument="--taxon" type="select" label="Origin of DNA">\n-            <option value="bacteria" selected="True">Bacteria</option>\n-            <option value="fungi">Fungi</option>\n-        </param>\n+        <conditional name="cond_taxon">\n+            <param argument="--taxon" type="select" label="Origin of DNA">\n+                <option value="bacteria" selected="True">Bacteria</option>\n+                <option value="fungi">Fungi</option>\n+            </param>\n+            <when value="bacteria">\n+                <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"\n+                    help="The \'error\' option will raise an error if genefinding is attempted. The \'none\' option will not run genefinding">\n+                    <option value="prodigal" selected="True">Prodigal</option>\n+                    <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>\n+                    <option value="glimmerhmm">GlimmerHMM</option>\n+                    <option value="none">None</option>\n+                    <option value="error">Error</option>\n+                </param>\n+            </when>\n+            <when value="fungi">\n+                <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"\n+                    help="The \'error\' option will raise an error if genefinding is attempted. The \'none\' option will not run genefinding">\n+                    <option value="glimmerhmm">GlimmerHMM</option>\n+                    <option value="none">None</option>\n+                    <option value="error">Error</option>\n+                </param>\n+                <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="False"\n+                       label="Motif based prediction of SM gene cluster regions" />\n+            </when>\n+        </conditional>\n \n-        <param argument="--input_type" t'..b'             help="Compare identified clusters against known subclusters responsible for synthesising precursors." />\n-        <param argument="--knownclusterblast" type="boolean" truevalue="--knownclusterblast" falsevalue="" checked="True"\n+        <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="True"\n                label="KnowCluster BLAST analysis"\n                help="Compare identified clusters against known gene clusters from the MIBiG database."/>\n-        <param argument="--smcogs" type="boolean" checked="True" truevalue="--smcogs" falsevalue=""\n+        <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue=""\n                label="Analysis of secondary metabolism gene families (smCOGs)"\n                help="Look for sec. met. clusters of orthologous groups."/>\n-        <param argument="--inclusive" type="boolean" truevalue="--inclusive" falsevalue="" checked="False"\n-               label="Inclusive ClusterFinder algorithm"\n-               help="Use inclusive ClusterFinder algorithm for additional cluster detection."/>\n-        <param argument="--borderpredict" type="boolean" truevalue="--borderpredict" falsevalue="" checked="False"\n-               label="Predict gene cluster borders with ClusterFinder"\n-               help="Use ClusterFinder algorithm to predict gene cluster borders."/>\n         <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True"\n-               label="Run active site finder module" />\n-        <param argument="--tta" type="boolean" truevalue="--tta" falsevalue="" checked="False"\n-               label="Run TTA codon detection module" />\n-        <param argument="--full_hmmer" type="boolean" truevalue="--full-hmmer" falsevalue="" checked="False"\n-               label="Run a whole-genome Pfam analysis" />\n+               label="Run active site finder analysus" />\n+        <param argument="-pfam2go" type="boolean" truevalue="-pfam2go" falsevalue="" checked="True"\n+               label="Run Pfam to Gene Ontology mapping module" />\n+        <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at" />\n+\n+        <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="False"\n+               label="Run a cluster-limited HMMer analysis" />\n+        <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="False"\n+               label="Run a whole-genome HMMer analysis" />\n+\n+        <param name="extra_cluster" type="select" label="Clusters">\n+            <option value="--cf-create-clusters" selected="True">Find extra clusters</option>\n+            <option value="--cf-borders-only">Only annotate borders of existing clusters</option>\n+        </param>\n \n         <param name="outputs" type="select" multiple="true" label="Outputs">\n             <option value="html" selected="True">HTML file</option>\n@@ -116,8 +145,14 @@\n         <test>\n             <param name="infile" value="sequence.gb"/>\n             <param name="outputs" value="html,gb"/>\n+            <param name="taxon" value="fungi"/>\n+            <param name="clusterhmmer" value="True"/>\n+            <param name="fullhmmer" value="True"/>\n+            <param name="extra_cluster" value="--cf-create-clusters"/>\n+            <param name="cassis" value="True"/>\n+            <param name="cb_general" value="True"/>\n             <output_collection name="genbank" type="list">\n-                <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" compare="sim_size" />\n+                <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" />\n                 <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/>\n             </output_collection>\n             <output name="html" file="index.2.html"/>\n'
b
diff -r 3f0077c88c16 -r 5784e268efca test-data/ARBH01000003.1.cluster001
--- a/test-data/ARBH01000003.1.cluster001 Sat Feb 10 02:37:49 2018 -0500
+++ b/test-data/ARBH01000003.1.cluster001 Sun Aug 09 10:15:12 2020 -0400
b
b'@@ -10,12 +10,15 @@\n             Amycolatopsis.\n FEATURES             Location/Qualifiers\n      source          1..3500\n-                     /organism="Amycolatopsis balhimycina FH 1894"\n-                     /mol_type="genomic DNA"\n-                     /strain="DSM 44591"\n                      /culture_collection="DSM:44591"\n                      /db_xref="taxon:1089545"\n+                     /mol_type="genomic DNA"\n+                     /organism="Amycolatopsis balhimycina FH 1894"\n+                     /strain="DSM 44591"\n      cluster         1..3500\n+                     /contig_edge="True"\n+                     /cutoff=20000\n+                     /extension=20000\n                      /note="Cluster number: 1"\n                      /note="Detection rule(s) for this cluster type: t1pks:\n                      ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS &\n@@ -23,16 +26,31 @@\n                      (tra_KS & PKS_AT));"\n                      /note="Monomers prediction: (mal)"\n                      /note="Structure image: structures/genecluster1.png"\n-                     /cutoff=20000\n-                     /extension=20000\n                      /product="t1pks"\n-                     /contig_edge="True"\n      CDS             3..3500\n                      /aSProdPred="mal"\n+                     /locus_tag="ctg1_1"\n                      /note="smCOG:\n                      SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score:\n                      64.2; E-value: 2.2e-19);"\n-                     /locus_tag="ctg1_1"\n+                     /sec_met="Type: t1pks"\n+                     /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,\n+                     bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,\n+                     bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,\n+                     bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,\n+                     bitscore: 162.1, seeds: 230)"\n+                     /sec_met="Kind: biosynthetic"\n+                     /sec_met="NRPS/PKS subtype: Type I Modular PKS"\n+                     /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:\n+                     1.4e-53. Score: 173.1; Predicted KR activity: active;\n+                     Predicted KR stereochemistry: A2;"\n+                     /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31.\n+                     Score: 97.8;"\n+                     /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value:\n+                     3e-179. Score: 587.9;"\n+                     /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value:\n+                     4e-80. Score: 260.9; Substrate specificity predictions: mal\n+                     (PKS signature), mal (Minowa), mal (consensus);"\n                      /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR\n                      APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL\n                      LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS\n@@ -54,81 +72,64 @@\n                      IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN\n                      GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH\n                      "\n-                     /sec_met="Type: t1pks"\n-                     /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,\n-                     bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,\n-                     bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,\n-                     bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,\n-                     bitscore: 162.1, seeds: 230)"\n-                     /sec_met="Kind: biosynthetic"\n-                     /sec_met="NRPS/PKS subtype: Type I Modular PKS"\n-                     /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:\n-                     1.4e-53. Score: 173.1; Predicted KR activity: active;\n-                     Predicted KR stereochemistry: A2;"\n-                     /sec_met="NRPS/'..b'              /score="260.9"\n+                     /specificity="PKS signature: mal"\n+                     /specificity="Minowa: mal"\n+                     /specificity="consensus: mal"\n                      /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW\n                      DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD\n                      ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV\n                      LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH"\n-                     /label="ctg1_1_AT1"\n-                     /asDomain_id="nrpspksdomains_ctg1_1_AT1"\n-                     /specificity="PKS signature: mal"\n-                     /specificity="Minowa: mal"\n-                     /specificity="consensus: mal"\n      CDS_motif       3033..3095\n-                     /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,\n-                     bit-score: 10.9)"\n+                     /aSTool="pksnrpsmotif"\n+                     /asDomain_id="nrpspksmotif_ctg1_1_0007"\n+                     /database="abmotifs"\n+                     /detection="hmmscan"\n+                     /evalue="3.20E-03"\n+                     /label="PKSI-AT-mM_m2"\n                      /locus_tag="ctg1_1"\n                      /motif="PKSI-AT-mM_m2"\n-                     /database="abmotifs"\n-                     /evalue="3.20E-03"\n-                     /asDomain_id="nrpspksmotif_ctg1_1_0007"\n-                     /detection="hmmscan"\n+                     /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,\n+                     bit-score: 10.9)"\n                      /score="10.9"\n+                     /translation="DETGYTQPALFAFEVALFRLL"\n+     CDS_motif       3105..3227\n                      /aSTool="pksnrpsmotif"\n-                     /translation="DETGYTQPALFAFEVALFRLL"\n-                     /label="PKSI-AT-mM_m2"\n-     CDS_motif       3105..3227\n+                     /asDomain_id="nrpspksmotif_ctg1_1_0008"\n+                     /database="abmotifs"\n+                     /detection="hmmscan"\n+                     /evalue="2.30E-22"\n+                     /label="PKSI-AT-M_m3"\n+                     /locus_tag="ctg1_1"\n+                     /motif="PKSI-AT-M_m3"\n                      /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,\n                      bit-score: 71.3)"\n-                     /locus_tag="ctg1_1"\n-                     /motif="PKSI-AT-M_m3"\n+                     /score="71.3"\n+                     /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"\n+     CDS_motif       3312..3350\n+                     /aSTool="pksnrpsmotif"\n+                     /asDomain_id="nrpspksmotif_ctg1_1_0009"\n                      /database="abmotifs"\n-                     /evalue="2.30E-22"\n-                     /asDomain_id="nrpspksmotif_ctg1_1_0008"\n                      /detection="hmmscan"\n-                     /score="71.3"\n-                     /aSTool="pksnrpsmotif"\n-                     /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"\n-                     /label="PKSI-AT-M_m3"\n-     CDS_motif       3312..3350\n+                     /evalue="4.70E-04"\n+                     /label="PKSI-AT-M_m5"\n+                     /locus_tag="ctg1_1"\n+                     /motif="PKSI-AT-M_m5"\n                      /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,\n                      bit-score: 13.4)"\n-                     /locus_tag="ctg1_1"\n-                     /motif="PKSI-AT-M_m5"\n-                     /database="abmotifs"\n-                     /evalue="4.70E-04"\n-                     /asDomain_id="nrpspksmotif_ctg1_1_0009"\n-                     /detection="hmmscan"\n                      /score="13.4"\n-                     /aSTool="pksnrpsmotif"\n                      /translation="AAVNGPESVVLAG"\n-                     /label="PKSI-AT-M_m5"\n ORIGIN\n         1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg\n        61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg\n'
b
diff -r 3f0077c88c16 -r 5784e268efca test-data/index.2.html
--- 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
[
b'@@ -1,273 +1,114 @@\n-<!doctype html>\n-<html>\n-  <head>\n-    <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title>\n-    <link rel="stylesheet" type="text/css" href="css/bacteria.css">\n-    <meta charset="utf-8">\n-  </head>\n-  <body>\n-    <div id="header">\n-      <div class="top-header">\n-        <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">\n-        <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>\n-            <span class="white">Version <span id="antismash-version">4.0.2</span></span>\n-        </span>\n-        <div id="icons">\n-          <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>\n-          <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a>\n-          <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a>\n-          <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a>\n-          <div id="downloadmenu">\n-            <ul id="downloadoptions">\n-            <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>\n-          </div>\n-        </div>\n-      </div>\n-      <div id="buttons">\n-        <span id="cluster-type">Select Gene Cluster:</span>\n-        <ul id="clusterbuttons">\n-          <li><div class="arrow-left" id="prev-cluster"></div></li>\n-          <li class="clbutton"><a href="#">Overview</a></li>\n-          <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>\n-        </ul>\n-      </div>\n-    </div>\n \n-    <!-- overview page -->\n-    <div class="page" id="overview">\n-      <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3>\n-      <table id="cluster-overview">\n-        <thead>\n-          <tr>\n-            <th>Cluster</th>\n-            <th>Type</th>\n-            <th>From</th>\n-            <th>To</th>\n-            <th>Most similar known cluster</th>\n-            <th>MIBiG BGC-ID</th>\n-          </tr>\n-        </thead>\n-        <tbody>\n-        <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>\n-      </table>\n-    </div>\n+<!doctype html>\n+<html lang="en">\n+<head>\n+  <meta charset="utf-8" />\n+  <title>input_tempfile - 0 region(s) - antiSMASH results</title>\n+  <style>img {width: 20px; height: 20px;}</style>\n+  <link rel="stylesheet" type="text/css" href="css/fungi.css">\n+  <meta property="og:title" content="input_tempfile - 0 record(s) - 0 region(s)" />\n+  <meta property="og:description" content="">\n+  <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/fungi_logo.png" />\n+  <meta property="og:image:alt" content="antiSMASH logo" />\n+  <meta property="og:image:width" content="600" />\n+  <meta property="og:image:height" content="600" />\n+  <meta property="og:url" content="https://fungismash.secondarymetabolites.org/upload/input_tempfile/index.html" />\n+  <meta property="og:type" content="website" />\n+  <meta name="twitter:card" content="summary" />\n+  <meta name="twitter:site" content="@an'..b'ter", text);\n-}\n-\n-$(document).ready(function() {\n-\n-    $("#download").click(toggle_downloadmenu);\n-\n-    $("#next-cluster").click(next_cluster);\n-    $("#prev-cluster").click(previous_cluster);\n-\n-    $(".clbutton").click(function() {\n-        /* Make sure that even if user missed the link and clicked the\n-           background we still have the correct anchor */\n-        var href = $(this).children().first().attr(\'href\');\n-\n-        if (href === undefined) {\n-            return;\n-        }\n-        window.location.href = href;\n+  <footer class="footer">\n+    <div class="container">\n+      <div>\n+        <img src="images/fungi_antismash_logo.svg" style="height:90px;width:unset;">\n+      </div>\n+      <div class="cite-me">\n+        If you have found antiSMASH useful, please <a href="https://fungismash.secondarymetabolites.org/#!/about">cite us</a>.\n+      </div>\n+      <div>\n+        <img src="images/fungi_antismash_icon.svg" style="height:100px;width:unset;">\n+      </div>\n+    </div>\n+  </footer>\n \n-        switch_to_cluster();\n-    }).mouseover(function() {\n-        /* Set the select cluster label text to cluster type */\n-        var classes = $(this).attr(\'class\').split(\' \');\n-        if (classes.length < 2) {\n-          return;\n-        }\n-        if (classes[1] == \'separator\') {\n-          return;\n-        }\n-        var cluster_type = map_type_to_desc(classes[1]);\n-        var label = $(\'#cluster-type\');\n-        label.data("orig_text", label.text());\n-        label.text(cluster_type + ":");\n-    }).mouseout(function() {\n-        /* and reset the select cluster label text */\n-        var label = $(\'#cluster-type\');\n-        label.text(label.data("orig_text"));\n-    });\n+  <script src="js/jquery.js"></script>\n+  <script src="js/antismash.js"></script>\n+  <script src="regions.js"></script>\n+  <script>\n+    $(document).ready(function() {\n+        viewer["start"](all_regions, details_data, recordData);\n+    })\n+  </script>\n \n-    $(\'.clusterblast-selector\').change(function() {\n-        var id = $(this).attr(\'id\').replace(\'-select\', \'\');\n-        var url = $(this).val();\n-        $.get(url, function(data) {\n-            $(\'#\' + id + \'-svg\').html(data);\n-            clusterblast.init(id + \'-svg\');\n-            //            id =\n-        }, \'html\');\n-        $(\'#\' + id + \'-download\').off(\'click\');\n-        $(\'#\' + id + \'-download\').click(function () {\n-            var url = $("#" + id + "-select").val();\n-            window.open(url, \'_blank\');\n-        });\n-    });\n-\n-    $(\'.domainalign-selector\').change(function() {\n-        var id = $(this).attr(\'id\').replace(\'-select\', \'\');\n-        var url = $(this).val();\n-        $.get(url, function(data) {\n-            $(\'#\' + id + \'-svg\').html(data);\n-            domainalign.init(id + \'-svg\');\n-            //            id =\n-        }, \'html\');\n-        $(\'#\' + id + \'-download\').off(\'click\');\n-        $(\'#\' + id + \'-download\').click(function () {\n-            var url = $("#" + id + "-select").val();\n-            window.open(url, \'_blank\');\n-        });\n-    });\n-\n-    $(\'.cluster-rules-header\').click(toggle_cluster_rules);\n-\n-    switch_to_cluster();\n-\n-});\n-    </script>\n-\n-  </body>\n+<svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink">\n+ <defs>\n+  <filter id="inset-shadow">\n+   <feOffset dx="-2" dy="-2"></feOffset>\n+   <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur>\n+   <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite>\n+   <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood>\n+   <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite>\n+   <feComponentTransfer in="shadow" result="shadow">\n+    <feFuncA type="linear" slope=".95"></feFuncA>\n+   </feComponentTransfer>\n+   <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite>\n+  </filter>\n+ </defs>\n+</svg>\n+</body>\n </html>\n\\ No newline at end of file\n'
b
diff -r 3f0077c88c16 -r 5784e268efca test-data/index.html
--- a/test-data/index.html Sat Feb 10 02:37:49 2018 -0500
+++ b/test-data/index.html Sun Aug 09 10:15:12 2020 -0400
[
b'@@ -1,273 +1,360 @@\n+\n <!doctype html>\n-<html>\n-  <head>\n-    <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title>\n-    <link rel="stylesheet" type="text/css" href="css/bacteria.css">\n-    <meta charset="utf-8">\n-  </head>\n-  <body>\n-    <div id="header">\n-      <div class="top-header">\n-        <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">\n-        <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>\n-            <span class="white">Version <span id="antismash-version">4.0.2</span></span>\n-        </span>\n-        <div id="icons">\n-          <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>\n-          <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a>\n-          <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a>\n-          <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a>\n-          <div id="downloadmenu">\n-            <ul id="downloadoptions">\n-            <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>\n-          </div>\n+<html lang="en">\n+<head>\n+  <meta charset="utf-8" />\n+  <title>input_tempfile - 1 region(s) - antiSMASH results</title>\n+  <style>img {width: 20px; height: 20px;}</style>\n+  <link rel="stylesheet" type="text/css" href="css/bacteria.css">\n+  <meta property="og:title" content="input_tempfile - 1 record(s) - 1 region(s)" />\n+  <meta property="og:description" content="">\n+  <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/bacteria_logo.png" />\n+  <meta property="og:image:alt" content="antiSMASH logo" />\n+  <meta property="og:image:width" content="600" />\n+  <meta property="og:image:height" content="600" />\n+  <meta property="og:url" content="https://antismash.secondarymetabolites.org/upload/input_tempfile/index.html" />\n+  <meta property="og:type" content="website" />\n+  <meta name="twitter:card" content="summary" />\n+  <meta name="twitter:site" content="@antismash_dev" />\n+</head>\n+\n+<body>\n+  <div id="header">\n+      <nav>\n+    <div class="main-link">\n+     <div>\n+        <a href="https://antismash.secondarymetabolites.org/">\n+          <img src="images/bacteria_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;">\n+        </a>\n+       </div>\n+       <div>\n+        <a href="https://antismash.secondarymetabolites.org/">\n+          antiSMASH version 5.1.2\n+        </a>\n+      </div>\n+    </div>\n+    <div class="custom-description"></div>\n+    <div class="ancillary-links">\n+      <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>\n+        <ul class="dropdown-options">\n+        \n+        <li><a href="input_tempfile.zip">Download all results</a></li>\n+        \n+          <li><a href="input_tempfile.gbk">Download GenBank summary file</a></li>\n+        \n+        </ul>\n+      </div>\n+      <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.org/#!/about"><img src="images/about.svg" alt="about"> &nbsp; About</a></div>\n+      <div class="ancillary-link"><a href="https://docs.antismash.secondarymetabolites.org/"><img src="images/help.svg" alt="help"> &nbsp; Help</a></div>\n+      <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.'..b' 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>\n+    </div>\n+  \n+  <div>\n+    <p>No matches found.</p>\n+  </div>\n+  \n+</div>\n+    </div>\n+     \n+    \n+  </div>\n \n-        switch_to_cluster();\n-    }).mouseover(function() {\n-        /* Set the select cluster label text to cluster type */\n-        var classes = $(this).attr(\'class\').split(\' \');\n-        if (classes.length < 2) {\n-          return;\n-        }\n-        if (classes[1] == \'separator\') {\n-          return;\n-        }\n-        var cluster_type = map_type_to_desc(classes[1]);\n-        var label = $(\'#cluster-type\');\n-        label.data("orig_text", label.text());\n-        label.text(cluster_type + ":");\n-    }).mouseout(function() {\n-        /* and reset the select cluster label text */\n-        var label = $(\'#cluster-type\');\n-        label.text(label.data("orig_text"));\n-    });\n+  <div class="sidepanel">\n+    <div class="sidepanel-details-headers">\n+    \n+     \n+    \n+     \n+    \n+     \n+    \n+    </div>\n+    \n+     \n+    \n+     \n+    \n+     \n+    \n+  </div>\n+\n+ </div>\n+\n+</div>\n+\n \n-    $(\'.clusterblast-selector\').change(function() {\n-        var id = $(this).attr(\'id\').replace(\'-select\', \'\');\n-        var url = $(this).val();\n-        $.get(url, function(data) {\n-            $(\'#\' + id + \'-svg\').html(data);\n-            clusterblast.init(id + \'-svg\');\n-            //            id =\n-        }, \'html\');\n-        $(\'#\' + id + \'-download\').off(\'click\');\n-        $(\'#\' + id + \'-download\').click(function () {\n-            var url = $("#" + id + "-select").val();\n-            window.open(url, \'_blank\');\n-        });\n-    });\n+  <footer class="footer">\n+    <div class="container">\n+      <div>\n+        <img src="images/bacteria_antismash_logo.svg" style="height:90px;width:unset;">\n+      </div>\n+      <div class="cite-me">\n+        If you have found antiSMASH useful, please <a href="https://antismash.secondarymetabolites.org/#!/about">cite us</a>.\n+      </div>\n+      <div>\n+        <img src="images/bacteria_antismash_icon.svg" style="height:100px;width:unset;">\n+      </div>\n+    </div>\n+  </footer>\n \n-    $(\'.domainalign-selector\').change(function() {\n-        var id = $(this).attr(\'id\').replace(\'-select\', \'\');\n-        var url = $(this).val();\n-        $.get(url, function(data) {\n-            $(\'#\' + id + \'-svg\').html(data);\n-            domainalign.init(id + \'-svg\');\n-            //            id =\n-        }, \'html\');\n-        $(\'#\' + id + \'-download\').off(\'click\');\n-        $(\'#\' + id + \'-download\').click(function () {\n-            var url = $("#" + id + "-select").val();\n-            window.open(url, \'_blank\');\n-        });\n-    });\n+  <script src="js/jquery.js"></script>\n+  <script src="js/antismash.js"></script>\n+  <script src="regions.js"></script>\n+  <script>\n+    $(document).ready(function() {\n+        viewer["start"](all_regions, details_data, recordData);\n+    })\n+  </script>\n \n-    $(\'.cluster-rules-header\').click(toggle_cluster_rules);\n-\n-    switch_to_cluster();\n-\n-});\n-    </script>\n-\n-  </body>\n+<svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink">\n+ <defs>\n+  <filter id="inset-shadow">\n+   <feOffset dx="-2" dy="-2"></feOffset>\n+   <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur>\n+   <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite>\n+   <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood>\n+   <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite>\n+   <feComponentTransfer in="shadow" result="shadow">\n+    <feFuncA type="linear" slope=".95"></feFuncA>\n+   </feComponentTransfer>\n+   <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite>\n+  </filter>\n+ </defs>\n+</svg>\n+</body>\n </html>\n\\ No newline at end of file\n'