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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit b10ab97380b0f2f5850138b9ddc03cd6afae1a9d
author brasset_jensen
date Fri, 30 Sep 2022 14:46:12 +0000
parents 11708af40030
children
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  <!DOCTYPE html>
  <html lang="en">
  <head>
  <meta charset="utf-8">
  <title>pipeline</title>
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  <meta name="description" content="">
  <meta name="author" content="">
  <!-- Le styles -->
  <link href="css/bootstrap.css" rel="stylesheet">
  <link href="css/bootstrap-table.css" rel="stylesheet">
  <style type="text/css">
  body {
    padding-top: 60px;
    padding-bottom: 40px;
  }
  div#page {
    width: 940px;
    background-color: #fff;
    margin: 0 auto;
    text-align: left;
    border-color: #fff;
    border-style: none solid solid;
    border-width: medium 1px 1px;
  }

  div.content {
   	display: none;
	  float: right;
	  width: 550px;
  }
  div.content a, div.navigation a {
    text-decoration: none;
   	color: #777;
  }
  div.content a:focus, div.content a:hover, div.content a:active {
    text-decoration: underline;
  }
  
  div.controls {
    margin-top: 5px;
	  height: 23px;
  }
  
  div.controls a {
	  padding: 5px;
  }
  div.ss-controls {
	  float: left;
  }
  div.nav-controls {
	  float: right;
  }
  div.slideshow-container {
	  position: relative;
	  clear: both;
	  height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
  }
  div.loader {
  	position: absolute;
  	top: 0;
  	left: 0;
    background-image: url('loader.gif');
    background-repeat: no-repeat;
    background-position: center;
  	width: 550px;
  	height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
  }
  div.slideshow {
    
  }
  
  div.slideshow span.image-wrapper {
	  display: block;
	  position: absolute;
	  top: 0;
	  left: 0;
  }
  div.slideshow a.advance-link {
	  display: block;
 	  width: 550px;
    height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
    line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
    text-align: center;
  }
  div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
    text-decoration: none;
  }
  div.slideshow img {
    vertical-align: middle;
	border: 1px solid #ccc;
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  div.image-title {
    font-weight: bold;
    font-size: 1.4em;
  }

  div.image-desc {
    line-height: 1.3em;
    padding-top: 12px;
  }
  div.navigation {

  }
  ul.thumbs {
	clear: both;
	margin: 0;
	padding: 0;
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  ul.thumbs li {
	float: none;
	padding: 0;
	margin: 0;
    list-style: none;
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  a.thumb {
	padding: 0;
	display: inline;
	border: none;
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  ul.thumbs li.selected a.thumb {
	color: #000;
    font-weight: bold;
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  a.thumb:focus {
	outline: none;
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  ul.thumbs img {
	border: none;
	display: block;
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  div.pagination {
	clear: both;
  }
  div.navigation div.top {
    margin-bottom: 12px;
	height: 11px;
  }
  div.navigation div.bottom {
    margin-top: 12px;
  }
  div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
	display: block;
	float: left;
    margin-right: 2px;
	padding: 4px 7px 2px 7px;
	border: 1px solid #ccc;
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  div.pagination a:hover {
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  div.pagination span.current {
    font-weight: bold;
    background-color: #000;
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	color: #fff;
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  div.pagination span.ellipsis {
	border: none;
	padding: 5px 0 3px 2px;
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  div.download {
	float: right;
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	position: relative;
	clear: left;
	height: 75px;
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  span.image-caption {
	display: block;
	position: absolute;
	width: 550px;
	top: 0;
	left: 0;
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  div.caption {
	padding: 12px;
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  /* Featurettes
  ------------------------- */

  .featurette {
  padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
  overflow: hidden; /* Vertically center images part 2: clear their floats. */
  text-align: center;
  }

  .featurette-p
  {
   text-align: left;
  }

  .featurette-image {
  margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
  width: 450px;
  height: auto;
  }

  </style>
  <link href="css/bootstrap-responsive.css" rel="stylesheet">
  </head>
  <body>
  
  <div class="navbar navbar-inverse navbar-fixed-top">
  <div class="navbar-inner">
  <div class="container">
  <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
  <span class="icon-bar"></span>
  <span class="icon-bar"></span>
  <span class="icon-bar"></span>
  </button>
  <a class="brand" href="report.txt">Report</a>
  <div class="nav-collapse collapse">
  <ul class="nav">
  <li class="active"><a href="reads-sample-small.fastq.html">reads-sample-small.fastq</a></li>
  </ul>
  </div><!--/.nav-collapse -->
  </div>
  </div>
  </div><div class="container"><p><a class="btn" href="reads-sample-small.fastq-sub.html">View details &raquo;</a></p></div>

  <div class="container">
  <div class="featurette">
  <h1>reads-sample-small.fastq</h1>
  <p class="featurette-p">
  <A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_sorted.bam">alignment (bam)</A><br/> 
<A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_minus.bedgraph">bedgraph minus strand</A><br/> 
<A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_plus.bedgraph">bedgraph plus strand</A><br/> 
<A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_unique_minus.bedgraph">bedgraph unique minus strand</A><br/> 
<A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_unique_plus.bedgraph">bedgraph unique plus strand</A><br/> 
<A HREF="reads-sample-small.fastq/genome//dup_mapnum.txt">mappers (txt)</A><br/> 
<A HREF="reads-sample-small.fastq/genome//distribution.txt">mappers size distribution (txt)</A><br/> 
<A HREF="reads-sample-small.fastq/genome//reads-sample-small.fastq_18-29_unique_sorted.bam">unique alignment (bam)</A><br/> 
<A HREF="reads-sample-small.fastq/genome//dup_unique.txt">unique mappers (txt)</A><br/> 
<A HREF="reads-sample-small.fastq/genome//dup_nonmapp.txt">unmapped (txt)</A><br/> 

  </p><img  class="featurette-image"  src="reads-sample-small.fastq/genome//distribution.png"/><br />
  </div>
  </div>
  <div class="container"><h2>mappers #: 3968</h2><h2>unique mappers #: 3963</h2> </div>

  <div id="page">
  <div id="container">
  <div class="each-gallery">
  <div id="gallery" class="content">
  <div id="controls0" class="controls"></div>
  <div class="slideshow-container">
  <div id="loading0" class="loader"></div>
  <div id="slideshow0" class="slideshow"></div>
  </div>
  <div id="caption0" class="caption-container">Uniquely mapped reads</div>
  </div>
  <div id="thumbs0" class="navigation">
  <input type="text" id="myInput0" onkeyup="search(this)" placeholder="Search for names...">
  <ul class="thumbs noscript">
  
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_1.png" title="chrom_1">chrom_1</a>
    </li>
    
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_2.png" title="chrom_2">chrom_2</a>
    </li>
    
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_3.png" title="chrom_3">chrom_3</a>
    </li>
    
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_4.png" title="chrom_4">chrom_4</a>
    </li>
    
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_5.png" title="chrom_5">chrom_5</a>
    </li>
    
    <li>
    <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/unique/chrom_6.png" title="chrom_6">chrom_6</a>
    </li>
    
  </ul>
  </div>
  </div>
  <div id="page">
  <div id="container">
  <div class="each-gallery">
  <div id="gallery" class="content">
  <div id="controls1" class="controls"></div>
  <div class="slideshow-container">
  <div id="loading1" class="loader"></div>
  <div id="slideshow1" class="slideshow"></div>
  </div>
  <div id="caption1" class="caption-container">Reads randomly assigned</div>
  </div>
  <div id="thumbs1" class="navigation">
  <input type="text" id="myInput1" onkeyup="search(this)" placeholder="Search for names...">
  <ul class="thumbs noscript">
  
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_1.png" title="chrom_1">chrom_1</a>
        </li>
        
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_2.png" title="chrom_2">chrom_2</a>
        </li>
        
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_3.png" title="chrom_3">chrom_3</a>
        </li>
        
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_4.png" title="chrom_4">chrom_4</a>
        </li>
        
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_5.png" title="chrom_5">chrom_5</a>
        </li>
        
        <li>
        <a class="thumb"  href="reads-sample-small.fastq/genome//Gviz/rand/chrom_6.png" title="chrom_6">chrom_6</a>
        </li>
        
  </ul>
  </div>
  <div style="clear: both;"></div></div>
  </div>
  </div>
  
  <!-- FOOTER -->
  <div class="container">
  <footer>
  
  </footer>
  </div>
  <!-- Le javascript
  ================================================== -->
  <!-- Placed at the end of the document so the pages load faster -->
  <script type="text/javascript" src="js/filter.js"></script>
  <script type="text/javascript" src="js/jquery.js"></script>
  <script type="text/javascript" src="js/jquery-1.3.2.js"></script>
  <script type="text/javascript" src="js/jquery.galleriffic.js"></script>
  <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>
  <script type="text/javascript" src="js/bootstrap-table.js"></script>
  <script type="text/javascript" src="js/bootstrap.min.js"></script>
  <script type="text/javascript">
  jQuery(document).ready(function($) {
    // We only want these styles applied when javascript is enabled
    $('div.navigation').css({'width' : '300px', 'float' : 'left'});
    $('div.content').css('display', 'block');
    
    $(".each-gallery").each(function(i){
      // Initially set opacity on thumbs and add
      // additional styling for hover effect on thumbs
        var onMouseOutOpacity = 0.67;
      $('#thumbs + i + ul.thumbs li').opacityrollover({
      mouseOutOpacity:   onMouseOutOpacity,
      mouseOverOpacity:  1.0,
      fadeSpeed:         'fast',
      exemptionSelector: '.selected'
      });
      
      // Initialize Advanced Galleriffic Gallery
      var gallery = $('#thumbs'+i).galleriffic({
      delay:                     2500,
      numThumbs:                 22,
      preloadAhead:              10,
      enableTopPager:            true,
      enableBottomPager:         true,
      maxPagesToShow:            7,
      imageContainerSel:         '#slideshow'+ i,
      controlsContainerSel:      '#controls' + i,
      captionContainerSel:       '#caption' + i,
      loadingContainerSel:       '#loading' + i,
      renderSSControls:          true,
      renderNavControls:         true,
      playLinkText:              'Play',
      pauseLinkText:             'Pause',
      prevLinkText:              '&lsaquo; Previous',
      nextLinkText:              'Next &rsaquo;',
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      prevPageLinkText:          '&lsaquo; Prev',
      enableHistory:             false,
      autoStart:                 false,
      syncTransitions:           true,
      defaultTransitionDuration: 900,
      onSlideChange:             function(prevIndex, nextIndex) {
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        this.fadeTo('fast', 1.0);
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      });
    });
  });
  </script>
  </body>
  </html>