diff test-data/test3_report.html @ 16:a3b35edea53a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd

--- a/test-data/test3_report.html	Thu Mar 02 10:38:54 2023 +0000
+++ b/test-data/test3_report.html	Tue Nov 12 12:46:19 2024 +0000
@@ -4060,7 +4060,7 @@
 
 
     <script type="text/javascript">
-        var colors = ["#FF0000","#0000FF"];
+        var colors = ["#FF0000"];
         var broken_scaffolds_labels = [];
     </script>
     <script type="text/javascript">
@@ -4181,7 +4181,7 @@
         $('#reference_name').show().find('.val').html(referenceName);
     }
 
-    if (report[0][0] == 'Genome statistics') {  // if first section is empty (no reference), swap it and w/o reference statistics
+    if (report[0][0] == 'Alignment-based statistics') {  // if first section is empty (no reference), swap it and w/o reference statistics
         var genomeMetrics = report[0][1];
         var isSectionEmpty = true;
         for (var index = 0; index < genomeMetrics.length; index++) {
@@ -4502,8 +4502,7 @@
                     QUAST
                 </h1>
                 <p class="page_subtitle">
-                    <b>Quality Assessment Tool for Genome Assemblies</b>
-                    by <a href="http://cab.spbu.ru" class='dark_bg_link'>CAB</a>
+                    <b><a href="http://quast.sf.net" class='dark_bg_link'>Quality Assessment Tool for Genome Assemblies</a></b>
                 </p>
             </div>
         </td>
@@ -4639,7 +4638,7 @@
 
         <div class='json-code'>
             <div id='total-report-json'>
-                {"date":"07 July 2022, Thursday, 16:55:14","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0","6650.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}
+                {"date":"12 November 2024, Tuesday, 11:22:11","assembliesNames":["contigs1_fna"],"referenceName":"","order":[0],"report":[["Alignment-based statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Per base quality",[{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00"],"isMain":true},{"metricName":"# N's","quality":"Less is better","values":[0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28"],"isMain":false}]],["K-mer-based statistics",[]],["BUSCO completeness",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}
             </div>
             <div id='qualities-json'>
                 {{ qualities }}
@@ -4649,7 +4648,7 @@
             </div>
 
             <div id="contigs-lengths-json">
-                {"filenames":["contigs1_fna","contigs2_fna"],"lists_of_lengths":[[3980,1610,1120],[6650]]}
+                {"filenames":["contigs1_fna"],"lists_of_lengths":[[3980,1610,1120]]}
             </div>
             <div id='assemblies-lengths-json'>
                 {{ assembliesLengths }}
@@ -4661,7 +4660,7 @@
                 {"tickX":1}
             </div>
             <div id='coord-nx-json'>
-                {"coord_x":[[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contigs1_fna","contigs2_fna"]}
+                {"coord_x":[[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0]],"filenames":["contigs1_fna"]}
             </div>
             <div id='coord-ngx-json'>
                 {{ coordNGx }}
@@ -4701,7 +4700,7 @@
                 {{ krona }}
             </div>
             <div id='gc-json'>
-                {"filenames":["contigs1_fna","contigs2_fna"],"reference_index":null,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,3,1,0,1,2,1,5,5,5,2,5,4,4,7,1,6,2,5,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,3,2,1,0,0,5,3,4,4,7,3,5,2,4,7,0,10,1,1,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
+                {"filenames":["contigs1_fna"],"reference_index":null,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,3,1,0,1,2,1,5,5,5,2,5,4,4,7,1,6,2,5,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
             </div>
             <div id='icarus-json'>
                 {"links":["icarus_viewers/contig_size_viewer.html"],"links_names":["View in Icarus contig browser"]}