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gatk-3.8/settings/helpTemplates/common.html

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Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-21 04:33:29 +08:00
<!--
~ Copyright (c) 2012, The Broad Institute
~
~ Permission is hereby granted, free of charge, to any person
~ obtaining a copy of this software and associated documentation
~ files (the "Software"), to deal in the Software without
~ restriction, including without limitation the rights to use,
~ copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the
~ Software is furnished to do so, subject to the following
~ conditions:
~
~ The above copyright notice and this permission notice shall be
~ included in all copies or substantial portions of the Software.
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
~ OTHER DEALINGS IN THE SOFTWARE.
-->
Implemented see also and version header
2011-07-25 04:10:17 +08:00
Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-21 04:33:29 +08:00
<#--
This file contains all the theming neccesary to present GATKDocs on the GATK website
Included are the paths to our bootstrap assets as well as helper functions to generate relevant links
Implemented see also and version header
2011-07-25 04:10:17 +08:00
Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-21 04:33:29 +08:00
-->
Implemented see also and version header
2011-07-25 04:10:17 +08:00
Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-21 04:33:29 +08:00
<#global siteRoot = "http://gsa-stage:8080/" />
<#global forum = "http://gatk.vanillaforums.com/" />
<#macro makeHeader title isIndex>
<?php ob_start(); ?>
<!DOCTYPE html>
<html lang='en'>
<head>
<meta charset='utf-8'>
<title>${title} documentation</title>
<meta name='viewport' content='width=device-width, initial-scale=1.0'>
<meta name='description' content=''>
<link type="text/css" rel="stylesheet" href="bootstrap.min.css">
<script src="jquery.min.js"></script>
<script src="bootstrap.min.js"></script>
<style>
@media (min-width: 980px) {
body {
padding-top : 60px;
}
</style>
</head>
<body>
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container-fluid">
<a class="brand" href="index.html">GATK Documentation</a>
</div>
</div>
</div>
<div class="container-fluid">
<?php
ob_clean();
include '../include/common.php';
printHeader("${title}", "Guides");
?>
<div class="row-fluid">
<#if isIndex>
<section class="span4">
<aside class="well">
<h2>About GATKdocs</h2>
<p>He is some text describing the docs, what it is and stuf...nalysis ready SNP and indel
calls
with hand filtering when VQSR is not possib. nalysis ready SNP and indel calls with hand
filtering when VQSR is not possib </p>
</aside>
</section>
<div class="span8">
</#if>
</#macro>
<#macro footerInfo>
<hr>
<p class="see-also">See also <a href="index.html">Documentation index</a> | <a
href="${siteRoot}">GATK Site</a> | <a
href="${forum}">GATK support forum</a></p>
<p class="version">GATK version ${version} built at ${timestamp}.</p>
</#macro>
<#macro pageFooter>
</div><!--/.span-->
</div><!--/.row-->
</body>
<?php printFooter();
ob_end_flush();
?>
</#macro>
<#macro getCategories map filter>
<style>
#sidenav .accordion-body a {
color : gray;
}
.accordion-body li {
list-style : none;
}
</style>
<ul class="nav nav-pills nav-stacked" id="sidenav">
<#list 0..(map?keys?size-1) as x>
<li><a data-toggle="collapse" data-parent="#sidenav"
href="#${map?keys[x]}">${map?keys[x].getDescription()}</a>
<div id="${map?keys[x]}"
<?php echo (in_array('${map?keys[x]}', $categories)) ? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
<ul>
<#assign items=map?values[x] />
<#if filter !="all" >
<#list items as datum>
<#if datum.group == filter>
<li><a href="${datum.filename}" rel="tooltip"
title="${datum.summary}">${datum.name}</a>
</li>
</#if>
</#list>
<#else>
<#list items as datum>
<li><a href="${datum.filename}" rel="tooltip"
title="${datum.summary}">${datum.name}</a>
</li>
</#list>
</#if>
</ul>
</div>
</li>
</#list>
</ul>
</#macro>