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Commit defa92ec authored by Yohan Jarosz's avatar Yohan Jarosz
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quick fix kronaplots

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lib/imp.html
+ 28
− 16
View file @ defa92ec
......@@ -48,22 +48,22 @@
<div id="block-stats" class="container-fluid">
<div id="tabs" role="tabpanel">
<div class="row">
<ul class="nav nav-tabs navbar-nav navbar-fixed-top navbar-inverse" role="tablist">
<a class="navbar-brand" href="#"> IMP <small>Integrated Metaomic Pipeline </small></a>
<li><a href="#preprocessing" aria-controls="preprocessing" role="tab" data-toggle="tab">Preprocessing</a></li>
<li><a href="#assembly" aria-controls="assembly" role="tab" data-toggle="tab">Assembly</a></li>
<li><a href="#mapping" aria-controls="mapping" role="tab" data-toggle="tab">Mapping</a></li>
<li><a href="#annotation" aria-controls="annotation" role="tab" data-toggle="tab">Annotation</a></li>
<li><a href="#variants" aria-controls="variants" role="tab" data-toggle="tab">Variants</a></li>
<li><a href="#ratio" aria-controls="ratio" role="tab" data-toggle="tab">Ratio</a></li>
<li><a href="#overview" aria-controls="overview" role="tab" data-toggle="tab">Workflow overview</a></li>
<li><a href="#configurations" aria-controls="configurations" role="tab" data-toggle="tab">Configuration</a></li>
<li><a href="#references" aria-controls="references" role="tab" data-toggle="tab">References</a></li>
<p class="navbar-text navbar-right"></p>
</ul>
<ul id="tabnav" class="nav nav-tabs navbar-nav navbar-fixed-top navbar-inverse" role="tablist">
<a class="navbar-brand" href="#"> IMP <small>Integrated Metaomic Pipeline </small></a>
<li><a href="#preprocessing" aria-controls="preprocessing" role="tab" data-toggle="tab">Preprocessing</a></li>
<li><a href="#assembly" aria-controls="assembly" role="tab" data-toggle="tab">Assembly</a></li>
<li><a href="#mapping" aria-controls="mapping" role="tab" data-toggle="tab">Mapping</a></li>
<li><a id="annottab" href="#annotation" aria-controls="annotation" role="tab" data-toggle="tab">Annotation</a></li>
<li><a href="#variants" aria-controls="variants" role="tab" data-toggle="tab">Variants</a></li>
<li><a href="#ratio" aria-controls="ratio" role="tab" data-toggle="tab">Ratio</a></li>
<li><a href="#overview" aria-controls="overview" role="tab" data-toggle="tab">Workflow overview</a></li>
<li><a href="#configurations" aria-controls="configurations" role="tab" data-toggle="tab">Configuration</a></li>
<li><a href="#references" aria-controls="references" role="tab" data-toggle="tab">References</a></li>
<p class="navbar-text navbar-right"></p>
</ul>
</div>
<div class="container">
<div id="wholecontent" class="container">
<div class="tab-content">
<!-- STATISTICS -->
......@@ -156,7 +156,19 @@
<!-- ANNOTATION -->
<div role="tabpanel" class="tab-pane fade" id="annotation">
<section id="annotation-section" class="row">
<div id='krona-plot'></div>
<div class="row">
<div class="page-header">
<h1>MG annotation <small>Kronaplot</small></h1>
</div>
<iframe id="MG-kronaplot"></iframe>
</div>
<div class="row">
<div class="page-header">
<h1>MT annotation <small>Kronaplot</small></h1>
</div>
<iframe id="MT-kronaplot"></iframe>
</div>
</section>
</div>
......
lib/imp.js
+ 36
− 7
View file @ defa92ec
......@@ -250,6 +250,20 @@ function renderSimpleCarousel(selector, path, files){
$('#' + selector + "-wrapper").append(carousel);
}
function renderIframeCarousel(selector, path, files){
var fpath = null, dt = null, sl = null;
var carousel = $(simple_carousel(selector));
var slides = $(carousel).find(".carousel-inner");
for(var idx in files){
fpath = path + '/' + files[idx];
sl = $("<div class='item'><iframe style='width:100%;height:100%' src='" + fpath + "'></iframe></div>");
if(idx == 0){
sl.addClass("active");
}
slides.append(sl);
}
$('#' + selector + "-wrapper").append(carousel);
}
// Trigger functions
......@@ -371,15 +385,30 @@ $('.right.carousel-control').click(function(){
$('#tabs li:first > a').tab('show');
//load html tables
$(".table-result").each(function(idx, node) {
var ident = node.id;
$("#" + ident).load("Analysis/results/" + ident + ".html", function() {
// $(".table-result").each(function(idx, node) {
// var ident = node.id;
// $("#" + ident).load("Analysis/results/" + ident + ".html", function() {
//
// });
// });
});
});
// //load krona plot
$("#MG-kronaplot").width( $('#wholecontent').width()).height( $('#wholecontent').height());
$("#MT-kronaplot").width( $('#wholecontent').width()).height( $('#wholecontent').height());
//load krona plot
$("#krona-plot").load("Analysis/results/MG.gene_kegg_krona.html", function() {
// $("#kronaplot").load("Analysis/results/MG.gene_kegg_krona.html", function() {
// console.log('loaded');
// });
// renderIframeCarousel('carousel-annotation', 'Analysis/results', [
// 'MG.gene_kegg_krona.html'
// ]);
$('#annottab').on('show.bs.tab', function (e) {
if($("#MG-kronaplot").attr('src') === undefined){
$("#MG-kronaplot").attr('src', 'Analysis/results/MG.gene_kegg_krona.html');
$("#MT-kronaplot").attr('src', 'Analysis/results/MT.gene_kegg_krona.html');
}
});
rules/Analysis/MGMT.rules
+ 1
− 4
View file @ defa92ec
......@@ -555,7 +555,7 @@ rule ANALYSIS_KRONA_PLOT_MT:
echo {input}
echo {output[0]}
python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[4]} -o {output[0]}
ktImportText -o {output[1]} {output[0]}
ktImportText -o {output[1]} {output[0]} -a
"""
rule ANALYSIS_MG_QUALITY_STATS:
......@@ -651,6 +651,3 @@ rule ANALYSIS_MT_PREPROCESSED_QUALITY_STATS:
ht2-stat --encode=sanger -q -P -t {THREADS} -o {P_OUT}/stats_after_preprocessing/MT -i {input} >> {log} 2>&1
ht2-stat-draw.pl --dir {P_OUT}/stats_after_preprocessing/MT >> {log} 2>&1
"""
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