gapsInCoverage/config.html at master · sch-sdgs/gapsInCoverage · GitHub

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<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <script type="text/javascript" src="/site_media/jquery/js/jquery-1.6.1.min.js"></script>
    <style type="text/css">
      #formwrap {
       line-height: 2em;
       background: #eef;
       margin: 10px;
       padding: 10px;
       height: 500px;
      }
      body {
       font-family: "Lucida Grande", "Lucida Sans Unicode", Verdana, Arial, Helvetica, sans-serif;
       font-size: 14px;
      }
      .center { margin-left:auto; margin-right:auto; }
      .help {cursor:help; border-bottom: 1px dotted #A9A9A9}
    </style>
    <script>
        $(function() {
            function populateLibType(selectorID) {
                $('#'+selectorID).empty();
                var runtypeUrl = '/rundb/api/v1/content/?format=json';
                var files=[];
                $.get( runtypeUrl, function(data) {
                    $.each( data.objects, function(intIndex, result){
                        //var bedfile = result.name;
                        //var type = result.upload_type;
                        var file_path = result.file;
                        var bedfile = file_path.split('/')[8];
                        if (files.indexOf(bedfile) <0) {
                            if (selectorID == "exonicregions") {
                                if (file_path.includes("exonic") && file_path.includes("detail")) {
                                    $('#' + selectorID).append("<option value='" + file_path + "'>" + bedfile + "</option>");
                                    files.push(bedfile);
                                }
                            }
                            if (selectorID == "targetregions") {
                                if (!bedfile.includes("exonic") && file_path.includes("detail")) {
                                    $('#' + selectorID).append("<option value='" + file_path + "'>" + bedfile + "</option>");
                                    files.push(bedfile);
                                }

                            }
                        }
                    });
                });
            }

            // populate Library Type selector
            populateLibType("targetregions");
            populateLibType("exonicregions");

        });
    </script>
</head>
<body>
 <form id="gapsInCoverage" name="gapsInCoverage">
     <div style="text-align:center">
         <h1>Gaps in Coverage Plugin</h1>
     </div>
        <table class="center" cellpadding="5px">
            <tr id="targetselect">
             <td><span class="help"
               title="Select the target regions (ROI) matching your reference and enriched fragment library">
               Targeted Regions:</span></td>
             <td><select id="targetregions" name="targetregions"><option value="">None</option></select></td> </tr>
            <tr id="exonselect">
             <td><span class="help"
               title="Select a BED file containing the exonic co-ordinates within target regions">
               Exonic Regions:</span></td>
             <td><select id="exonicregions" name="exonicregions"></select></td> </tr>
            <tr id="introncov">
             <td><span class="help"
               title="Specify the minimum number of reads for which a base in an intron is considered sufficiently covered. Bases with coverage below this value will be considered 'gaps'">
               Min. Intron Coverage:</span></td>
             <td><input type="text" size=6 id="minintroncov" name="minintroncov" value=30></select></td> </tr>
            <tr id="exoncov">
             <td><span class="help"
               title="Specify the minimum number of reads in exon regions for which a base is considered sufficiently covered. Bases with coverage below this value will be considered 'gaps'">
               Min. Exon Coverage:</span></td>
             <td><input type="text" size=6 id="minexoncov" name="minexoncov" value=50></select></td> </tr>
        </table>
 </form>
</body>
</html>