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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 Categories. We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything. Tools can be hidden from GATKdocs with the @Hidden annotation Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 04:52:06 +08:00
<#global siteRoot = "http://www.broadinstitute.org/gatk/" />
Refactored GATKDocs categories some more ( GSATDG-62 ) -- Renamed ValidatePileup to CheckPileup since validation is reserved word -- Renamed AlignmentValidation to CheckAlignment (same as above) -- Refactored category definitions to use constants defined in HelpConstants -- Fixed a couple of minor typos and an example error -- Reorganized the GATKDocs index template to use supercategories -- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
2013-02-13 05:27:18 +08:00
<#global guideIndex = "http://www.broadinstitute.org/gatk/guide/" />
<#global forum = "http://gatkforums.broadinstitute.org/" />
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
<#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;
}
Removed Categories. We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything. Tools can be hidden from GATKdocs with the @Hidden annotation Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 04:52:06 +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
</style>
Various documentation improvements - Edited intervals merging docs for correctness & clarity - Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests) - Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs - Moved GenotypeGVCFs to Variant Discovery category and clarified a few points - Clarified that the -resource argument depends on using the -V:tag format - Clarified how the pcr indel model works - Added caveat for -U ALLOW_N_CIGAR_READS - Added MathJax support for displaying equations in GATKDocs - Updated HC example commands and caveats
2014-05-22 00:35:22 +08:00
<!-- MathJax / MathML support for displaying equations -->
<script type='text/x-mathjax-config'>
MathJax.Hub.Config({
TeX: { equationNumbers: { autoNumber: 'AMS' } }
});
</script>
<script type='text/javascript' src='http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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
</head>
<body>
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container-fluid">
Tweaked gatkdocs index template
2013-11-20 04:05:41 +08:00
<a class="brand" href="index.html">GATK | Tool Documentation</a>
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
</div>
</div>
</div>
<div class="container-fluid">
<?php
Removed Categories. We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything. Tools can be hidden from GATKdocs with the @Hidden annotation Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 04:52:06 +08:00
// Output Buffering allows for the website to inject a different header
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
ob_clean();
include '../include/common.php';
printHeader("${title}", "Guides");
?>
<div class="row-fluid">
<#if isIndex>
Added the ability to update the Forum GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists. More changes were made to the GATKDocs. Works nicely with bootstrap on and offline. Cleaned up the code as well Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-24 04:44:53 +08:00
<?php printGATKDocsNav(); ?>
<div class="span9">
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
</#if>
</#macro>
<#macro footerInfo>
<hr>
Refactored GATKDocs categories some more ( GSATDG-62 ) -- Renamed ValidatePileup to CheckPileup since validation is reserved word -- Renamed AlignmentValidation to CheckAlignment (same as above) -- Refactored category definitions to use constants defined in HelpConstants -- Fixed a couple of minor typos and an example error -- Reorganized the GATKDocs index template to use supercategories -- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
2013-02-13 05:27:18 +08:00
<p class="see-also">See also
<a href="${guideIndex}">Guide Index</a> |
Tweaked gatkdocs index template
2013-11-20 04:05:41 +08:00
<a href="index.html">Tool Documentation Index</a> |
Refactored GATKDocs categories some more ( GSATDG-62 ) -- Renamed ValidatePileup to CheckPileup since validation is reserved word -- Renamed AlignmentValidation to CheckAlignment (same as above) -- Refactored category definitions to use constants defined in HelpConstants -- Fixed a couple of minor typos and an example error -- Reorganized the GATKDocs index template to use supercategories -- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
2013-02-13 05:27:18 +08:00
<a href="${forum}">Support Forum</a>
</p>
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
Assorted fixes and improvements to gatkdocs -Added docs for ERC mode in HC -Move RecalibrationPerformance walker since to private since it is experimental and unsupported -Updated VR docs and restored percentBad/numBad (but @Hidden) to enable deprecation alert if users try to use them -Improved error msg for conflict between per-interval aggregation and -nt -Minor clean up in exception docs -Added Toy Walkers category for devs and dev supercat (to build out docs for developers) -Added more detailed info to GenotypeConcordance doc based on Chris forum post -Added system to include min/max argument values in gatkdocs (build gatkdocs with 'ant gatkdocs' to test it, see engine and DoC args for in situ examples) -Added tentative min/max argument annotations to DepthOfCoverage and CommandLineGATK arguments (and improved docs while at it) -Added gotoDev annotation to GATKDocumentedFeature to track who is the go-to person in GSA for questions & issues about specific walkers/tools (now discreetly indicated in each gatkdoc)
2013-12-11 02:19:53 +08:00
<p class="version">GATK version ${version} built at ${timestamp}.
<#-- closing P tag in next macro -->
</#macro>
<#macro footerClose>
<#-- ugly little hack to enable adding tool-specific info inline -->
</p>
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
</#macro>
<#macro pageFooter>
</div><!--/.span-->
</div><!--/.row-->
</body>
<?php printFooter();
ob_end_flush();
?>
</#macro>
Removed Categories. We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything. Tools can be hidden from GATKdocs with the @Hidden annotation Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 04:52:06 +08:00
<#macro getCategories groups>
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
<style>
#sidenav .accordion-body a {
color : gray;
}
.accordion-body li {
list-style : none;
}
</style>
<ul class="nav nav-pills nav-stacked" id="sidenav">
Refactored GATKDocs categories some more ( GSATDG-62 ) -- Renamed ValidatePileup to CheckPileup since validation is reserved word -- Renamed AlignmentValidation to CheckAlignment (same as above) -- Refactored category definitions to use constants defined in HelpConstants -- Fixed a couple of minor typos and an example error -- Reorganized the GATKDocs index template to use supercategories -- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
2013-02-13 05:27:18 +08:00
<#assign seq = ["engine", "tools", "utilities", "other"]>
<#list seq as supercat>
<hr>
<#list groups?sort_by("name") as group>
<#if group.supercat == supercat>
<li><a data-toggle="collapse" data-parent="#sidenav" href="#${group.id}">${group.name}</a>
<div id="${group.id}"
<?php echo ($group == '${group.name}')? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
<ul>
<#list data as datum>
<#if datum.group == group.name>
<li>
<a href="${datum.filename}">${datum.name}</a>
</li>
</#if>
</#list>
</ul>
</div>
</li>
</#if>
</#list>
</#list>
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
</ul>
</#macro>