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gatk-3.8/settings/helpTemplates/generic.template.html

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V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-22 03:20:34 +08:00
<#macro argumentlist name myargs>
<#if myargs?size != 0>
Walker index html now emited.
2011-07-22 04:01:54 +08:00
<tr><th colspan="4" align="left">${name}</th></tr>
V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-22 03:20:34 +08:00
<#list myargs as arg>
<tr>
<td><a href="#${arg.name}">${arg.name}</a></td>
<td><a href="#${arg.name}">${arg.synonyms}</a></td>
<td>${arg.type}</td>
<td>${arg.summary}</td>
</tr>
<#--
<td>${arg.required}</td>
-->
</#list>
</#if>
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 12:18:07 +08:00
</#macro>
V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-22 03:20:34 +08:00
<#macro argumentDetails arg>
<h3><a name="${arg.name}">${arg.name} / ${arg.synonyms}</a></h3>
Summary: ${arg.summary}<br>
Attributes: ${arg.attributes}<br>
Type: ${arg.type}<br>
Options: ${arg.options}<br>
Details: ${arg.fulltext}<br>
</#macro>
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 12:18:07 +08:00
<html>
<head>
<title>${name} documentation</title>
</head>
<body>
<h1>${name}<h1>
<h2>Summary</h2>
${summary}
<#if author??>
<h2>Author</h2>
${author}
</#if>
<h2>Description</h2>
${description}
Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
2011-07-24 10:07:30 +08:00
V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-22 03:20:34 +08:00
<#-- Create the argument summary -->
Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
2011-07-24 10:07:30 +08:00
<#if arguments.all?size != 0>
<hr>
<h2>Feature specific arguments</h2>
<table border="1" cellpadding="2">
<tr>
<th>Name</th>
<th>Synonyms</th>
<th>Type</th>
<th>Summary</th>
</tr>
<@argumentlist name="Required" myargs=arguments.required/>
<@argumentlist name="Optional" myargs=arguments.optional/>
<@argumentlist name="Hidden" myargs=arguments.hidden/>
<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
</table>
</#if>
V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-22 03:20:34 +08:00
Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
2011-07-24 10:07:30 +08:00
<#-- Create references to related capabilities if appropriate -->
<#if extradocs?size != 0>
<hr>
<h2>Related capabilities</h2>
The arguments described in the entries below can be supplied to this tool to modify
its behavior. For example, the -L argument directs the GATK engine restricts processing
to specific genomic intervals. This capability is available to all GATK walkers.
<ul>
<#list extradocs as extradoc>
<li><a href="${extradoc.filename}">${extradoc.name}</a></li>
</#list>
</ul>
</#if>
<#-- List all of the -->
<#if arguments.all?size != 0>
<hr>
<#-- Create the argument details -->
<h2>Argument details</h2>
<#list arguments.all as arg>
<@argumentDetails arg=arg/>
</#list>
</#if>
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 12:18:07 +08:00
</body>
</html>