#
# xhtml11.conf
#
# Asciidoc configuration file.
# xhtml11 backend, generates XHTML 1.1 conformant markup.
#

[miscellaneous]
outfilesuffix=.html

[attributes]
basebackend=html
basebackend-html=
basebackend-xhtml11=

[replacements2]
# Line break.
(?m)^(.*)\s\+$=\1<br />

[replacements]
ifdef::asciidoc7compatible[]
# Superscripts.
\^(.+?)\^=<sup>\1</sup>
# Subscripts.
~(.+?)~=<sub>\1</sub>
endif::asciidoc7compatible[]

[ruler-blockmacro]
<hr />

[pagebreak-blockmacro]
<div style="page-break-after:always"></div>

[blockdef-pass]
asciimath-style=template="asciimathblock",subs=()
latexmath-style=template="latexmathblock",subs=()

[macros]
# math macros.
# Special characters are escaped in HTML math markup.
(?su)[\\]?(?P<name>asciimath|latexmath):(?P<subslist>\S*?)\[(?P<passtext>.*?)(?<!\\)\]=[specialcharacters]
(?u)^(?P<name>asciimath|latexmath)::(?P<subslist>\S*?)(\[(?P<passtext>.*?)\])$=#[specialcharacters]

[asciimath-inlinemacro]
`{passtext}`

[asciimath-blockmacro]
<div class="mathblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="content">
<div class="title">{title}</div>
`{passtext}`
</div></div>

[asciimathblock]
<div class="mathblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="content">
<div class="title">{title}</div>
`|`
</div></div>

[latexmath-inlinemacro]
{passtext}

[latexmath-blockmacro]
<div class="mathblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="content">
<div class="title">{title}</div>
{passtext}
</div></div>

[latexmathblock]
<div class="mathblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="content">
<div class="title">{title}</div>
|
</div></div>

[image-inlinemacro]
<span class="image{role? {role}}">
<a class="image" href="{link}">
{data-uri%}<img src="{imagesdir=}{imagesdir?/}{target}" alt="{alt={target}}"{width? width="{width}"}{height? height="{height}"}{title? title="{title}"} />
{data-uri#}<img alt="{alt={target}}"{width? width="{width}"}{height? height="{height}"}{title? title="{title}"} src="data:image/{eval:os.path.splitext(r'{target}')[1][1:]};base64,
{data-uri#}{sys3:"{python}" -u -c "import base64,sys; base64.encode(sys.stdin,sys.stdout)" < "{eval:os.path.join(r"{indir={outdir}}",r"{imagesdir=}",r"{target}")}"}" />
{link#}</a>
</span>

[image-blockmacro]
<div class="imageblock{style? {style}}{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}{align? style="text-align:{align};"}{float? style="float:{float};"}>
<div class="content">
<a class="image" href="{link}">
{data-uri%}<img src="{imagesdir=}{imagesdir?/}{target}" alt="{alt={target}}"{width? width="{width}"}{height? height="{height}"} />
{data-uri#}<img alt="{alt={target}}"{width? width="{width}"}{height? height="{height}"} src="data:image/{eval:os.path.splitext(r'{target}')[1][1:]};base64,
{data-uri#}{sys:"{python}" -u -c "import base64,sys; base64.encode(sys.stdin,sys.stdout)" < "{eval:os.path.join(r"{indir={outdir}}",r"{imagesdir=}",r"{target}")}"}" />
{link#}</a>
</div>
<div class="title">{caption={figure-caption} {counter:figure-number}. }{title}</div>
</div>

[unfloat-blockmacro]
<div style="clear:both;"></div>

[toc-blockmacro]
template::[toc]

[indexterm-inlinemacro]
# Index term.
{empty}

[indexterm2-inlinemacro]
# Index term.
# Single entry index term that is visible in the primary text flow.
{1}

[footnote-inlinemacro]
# footnote:[<text>].
<span class="footnote"><br />[{0}]<br /></span>

[footnoteref-inlinemacro]
# footnoteref:[<id>], create reference to footnote.
{2%}<span class="footnoteref"><br /><a href="#_footnote_{1}">[{1}]</a><br /></span>
# footnoteref:[<id>,<text>], create footnote with ID.
{2#}<span class="footnote" id="_footnote_{1}"><br />[{2}]<br /></span>

[callout-inlinemacro]
ifndef::icons[]
<b>&lt;{index}&gt;</b>
endif::icons[]
ifdef::icons[]
ifndef::data-uri[]
<img src="{icon={iconsdir}/callouts/{index}.png}" alt="{index}" />
endif::data-uri[]
ifdef::data-uri[]
<img alt="{index}" src="data:image/png;base64,
{sys:"{python}" -u -c "import base64,sys; base64.encode(sys.stdin,sys.stdout)" < "{eval:os.path.join(r"{indir={outdir}}",r"{icon={iconsdir}/callouts/{index}.png}")}"}" />
endif::data-uri[]
endif::icons[]

# Comment line macros.
[comment-inlinemacro]
{showcomments#}<br /><span class="comment">{passtext}</span><br />

[comment-blockmacro]
{showcomments#}<p><span class="comment">{passtext}</span></p>

[literal-inlinemacro]
# Inline literal.
<tt>{passtext}</tt>

# List tags.
[listtags-bulleted]
list=<div class="ulist{style? {style}}{compact-option? compact}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<ul>|</ul></div>
item=<li>|</li>
text=<p>|</p>

[listtags-numbered]
# The start attribute is not valid XHTML 1.1 but all browsers support it.
list=<div class="olist{style? {style}}{compact-option? compact}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<ol class="{style}"{start? start="{start}"}>|</ol></div>
item=<li>|</li>
text=<p>|</p>

[listtags-labeled]
list=<div class="dlist{compact-option? compact}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<dl>|</dl></div>
entry=
label=
term=<dt class="hdlist1{strong-option? strong}">|</dt>
item=<dd>|</dd>
text=<p>|</p>

[listtags-horizontal]
list=<div class="hdlist{compact-option? compact}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<table>{labelwidth?<col width="{labelwidth}%" />}{itemwidth?<col width="{itemwidth}%" />}|</table></div>
label=<td class="hdlist1{strong-option? strong}">|</td>
term=|<br />
entry=<tr>|</tr>
item=<td class="hdlist2">|</td>
text=<p style="margin-top: 0;">|</p>

[listtags-qanda]
list=<div class="qlist{style? {style}}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<ol>|</ol></div>
entry=<li>|</li>
label=
term=<p><em>|</em></p>
item=
text=<p>|</p>

[listtags-callout]
ifndef::icons[]
list=<div class="colist{style? {style}}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<ol>|</ol></div>
item=<li>|</li>
text=<p>|</p>
endif::icons[]
ifdef::icons[]
list=<div class="colist{style? {style}}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<table>|</table></div>
ifndef::data-uri[]
item=<tr><td><img src="{iconsdir}/callouts/{listindex}.png" alt="{listindex}" /></td><td>|</td></tr>
endif::data-uri[]
ifdef::data-uri[]
item=<tr><td><img alt="{listindex}" src="data:image/png;base64, {sys:"{python}" -u -c "import base64,sys; base64.encode(sys.stdin,sys.stdout)" < "{eval:os.path.join(r"{indir={outdir}}",r"{icon={iconsdir}/callouts/{listindex}.png}")}"}" /></td><td>|</td></tr>
endif::data-uri[]
text=|
endif::icons[]

[listtags-glossary]
list=<div class="dlist{style? {style}}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<dl>|</dl></div>
label=
entry=
term=<dt>|</dt>
item=<dd>|</dd>
text=<p>|</p>

[listtags-bibliography]
list=<div class="ulist{style? {style}}{role? {role}}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<ul>|</ul></div>
item=<li>|</li>
text=<p>|</p>

[tags]
# Quoted text.
emphasis=<em>{1?<span class="{1}">}|{1?</span>}</em>
strong=<strong>{1?<span class="{1}">}|{1?</span>}</strong>
monospaced=<tt>{1?<span class="{1}">}|{1?</span>}</tt>
singlequoted={lsquo}{1?<span class="{1}">}|{1?</span>}{rsquo}
doublequoted={ldquo}{1?<span class="{1}">}|{1?</span>}{rdquo}
unquoted={1?<span class="{1}">}|{1?</span>}
superscript=<sup>{1?<span class="{1}">}|{1?</span>}</sup>
subscript=<sub>{1?<span class="{1}">}|{1?</span>}</sub>

ifdef::deprecated-quotes[]
# Override with deprecated quote attributes.
emphasis={role?<span class="{role}">}<em{1,2,3? style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?"}>|</em>{role?</span>}
strong={role?<span class="{role}">}<strong{1,2,3? style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?"}>|</strong>{role?</span>}
monospaced={role?<span class="{role}">}<tt{1,2,3? style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?"}>|</tt>{role?</span>}
singlequoted={role?<span class="{role}">}{1,2,3?<span style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?">}{amp}#8216;|{amp}#8217;{1,2,3?</span>}{role?</span>}
doublequoted={role?<span class="{role}">}{1,2,3?<span style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?">}{amp}#8220;|{amp}#8221;{1,2,3?</span>}{role?</span>}
unquoted={role?<span class="{role}">}{1,2,3?<span style="{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}">}|{1,2,3?</span>}{role?</span>}
superscript={role?<span class="{role}">}<sup{1,2,3? style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?"}>|</sup>{role?</span>}
subscript={role?<span class="{role}">}<sub{1,2,3? style="}{1?color:{1};}{2?background-color:{2};}{3?font-size:{3}em;}{1,2,3?"}>|</sub>{role?</span>}
endif::deprecated-quotes[]

# Inline macros
[http-inlinemacro]
<a href="{name}:{target}">{0={name}:{target}}</a>
[https-inlinemacro]
<a href="{name}:{target}">{0={name}:{target}}</a>
[ftp-inlinemacro]
<a href="{name}:{target}">{0={name}:{target}}</a>
[file-inlinemacro]
<a href="{name}:{target}">{0={name}:{target}}</a>
[irc-inlinemacro]
<a href="{name}:{target}">{0={name}:{target}}</a>
[mailto-inlinemacro]
<a href="mailto:{target}">{0={target}}</a>
[link-inlinemacro]
<a href="{target}">{0={target}}</a>
[callto-inlinemacro]
<a href="{name}:{target}">{0={target}}</a>
# anchor:id[text]
[anchor-inlinemacro]
<a id="{target}"></a>
# [[id,text]]
[anchor2-inlinemacro]
<a id="{1}"></a>
# [[[id]]]
[anchor3-inlinemacro]
<a id="{1}"></a>[{1}]
# xref:id[text]
[xref-inlinemacro]
<a href="#{target}">{0=[{target}]}</a>
# <<id,text>>
[xref2-inlinemacro]
<a href="#{1}">{2=[{1}]}</a>

# Special word substitution.
[emphasizedwords]
<em>{words}</em>
[monospacedwords]
<tt>{words}</tt>
[strongwords]
<strong>{words}</strong>

# Paragraph substitution.
[paragraph]
<div class="paragraph{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>{title?<div class="title">{title}</div>}<p>
|
</p></div>

[admonitionparagraph]
template::[admonitionblock]

# Delimited blocks.
[listingblock]
<div class="listingblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{caption=}{title}</div>
<div class="content">
<pre><tt>
|
</tt></pre>
</div></div>

[literalblock]
<div class="literalblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{title}</div>
<div class="content">
<pre><tt>
|
</tt></pre>
</div></div>

[sidebarblock]
<div class="sidebarblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="content">
<div class="title">{title}</div>
|
</div></div>

[openblock]
<div class="openblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{title}</div>
<div class="content">
|
</div></div>

[partintroblock]
template::[openblock]

[abstractblock]
template::[quoteblock]

[quoteblock]
<div class="quoteblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{title}</div>
<div class="content">
|
</div>
<div class="attribution">
<em>{citetitle}</em>{attribution?<br />}
&#8212; {attribution}
</div></div>

[verseblock]
<div class="verseblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{title}</div>
<pre class="content">
|
</pre>
<div class="attribution">
<em>{citetitle}</em>{attribution?<br />}
&#8212; {attribution}
</div></div>

[exampleblock]
<div class="exampleblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<div class="title">{caption={example-caption} {counter:example-number}. }{title}</div>
<div class="content">
|
</div></div>

[admonitionblock]
<div class="admonitionblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<table><tr>
<td class="icon">
{data-uri%}{icons#}<img src="{icon={iconsdir}/{name}.png}" alt="{caption}" />
{data-uri#}{icons#}<img alt="{caption}" src="data:image/png;base64,
{data-uri#}{icons#}{sys:"{python}" -u -c "import base64,sys; base64.encode(sys.stdin,sys.stdout)" < "{eval:os.path.join(r"{indir={outdir}}",r"{icon={iconsdir}/{name}.png}")}"}" />
{icons%}<div class="title">{caption}</div>
</td>
<td class="content">
<div class="title">{title}</div>
|
</td>
</tr></table>
</div>

# Tables.
[tabletags-default]
colspec=<col{autowidth-option! width="{colpcwidth}%"} />
bodyrow=<tr>|</tr>
headdata=<th {colspan@1::colspan="{colspan}" }{rowspan@1::rowspan="{rowspan}" }align="{halign}" valign="{valign}">|</th>
bodydata=<td {colspan@1::colspan="{colspan}" }{rowspan@1::rowspan="{rowspan}" }align="{halign}" valign="{valign}">|</td>
paragraph=<p class="table">|</p>

[tabletags-header]
paragraph=<p class="table header">|</p>

[tabletags-emphasis]
paragraph=<p class="table"><em>|</em></p>

[tabletags-strong]
paragraph=<p class="table"><strong>|</strong></p>

[tabletags-monospaced]
paragraph=<p class="table"><tt>|</tt></p>

[tabletags-verse]
bodydata=<td {colspan@1::colspan="{colspan}" }{rowspan@1::rowspan="{rowspan}" }align="{halign}" valign="{valign}"><div class="verse">|</div></td>
paragraph=

[tabletags-literal]
bodydata=<td {colspan@1::colspan="{colspan}" }{rowspan@1::rowspan="{rowspan}" }align="{halign}" valign="{valign}"><div class="literal"><pre><tt>|</tt></pre></div></td>
paragraph=

[tabletags-asciidoc]
bodydata=<td {colspan@1::colspan="{colspan}" }{rowspan@1::rowspan="{rowspan}" }align="{halign}" valign="{valign}"><div>|</div></td>
paragraph=

[table]
<div class="tableblock{role? {role}}{unbreakable-option? unbreakable}"{id? id="{id}"}>
<table rules="{grid=all}"
style="margin-left:{align@left:0}{align@center|right:auto}; margin-right:{align@left|center:auto}{align@right:0};"
style="float:{float};"
{autowidth-option%}width="{tablepcwidth}%"
{autowidth-option#}{width#width="{tablepcwidth}%"}
frame="{frame%border}"
frame="{frame@topbot:hsides}{frame@all:border}{frame@none:void}{frame@sides:vsides}"
cellspacing="0" cellpadding="4">
<caption class="title">{caption={table-caption} {counter:table-number}. }{title}</caption>
{colspecs}
{headrows#}<thead>
{headrows}
{headrows#}</thead>
{footrows#}<tfoot>
{footrows}
{footrows#}</tfoot>
<tbody>
{bodyrows}
</tbody>
</table>
</div>

#--------------------------------------------------------------------
# Deprecated old table definitions.
#

[miscellaneous]
# Screen width in pixels.
pagewidth=800
pageunits=

[old_tabledef-default]
template=old_table
colspec=<col width="{colwidth}{pageunits}" />
bodyrow=<tr>|</tr>
headdata=<th align="{colalign}">|</th>
footdata=<td align="{colalign}">|</td>
bodydata=<td align="{colalign}">|</td>

[old_table]
<div class="tableblock"{id? id="{id}"}>
<table rules="{grid=none}"
frame="{frame%hsides}"
frame="{frame@topbot:hsides}{frame@all:border}{frame@none:void}{frame@sides:vsides}"
cellspacing="0" cellpadding="4">
<caption class="title">{caption={table-caption}}{title}</caption>
{colspecs}
{headrows#}<thead>
{headrows}
{headrows#}</thead>
{footrows#}<tfoot>
{footrows}
{footrows#}</tfoot>
<tbody valign="top">
{bodyrows}
</tbody>
</table>
</div>

# End of deprecated old table definitions.
#--------------------------------------------------------------------

[floatingtitle]
<h{level@0:1}{level@1:2}{level@2:3}{level@3:4}{level@4:5}{id? id="{id}"} class="float">{title}</h{level@0:1}{level@1:2}{level@2:3}{level@3:4}{level@4:5}>

[preamble]
# Untitled elements between header and first section title.
<div id="preamble">
<div class="sectionbody">
|
</div>
</div>

# Document sections.
[sect0]
<h1{id? id="{id}"}>{title}</h1>
|

[sect1]
<div class="sect1{style? {style}}{role? {role}}">
<h2{id? id="{id}"}>{numbered?{sectnum} }{title}</h2>
<div class="sectionbody">
|
</div>
</div>

[sect2]
<div class="sect2{style? {style}}{role? {role}}">
<h3{id? id="{id}"}>{numbered?{sectnum} }{title}</h3>
|
</div>

[sect3]
<div class="sect3{style? {style}}{role? {role}}">
<h4{id? id="{id}"}>{numbered?{sectnum} }{title}</h4>
|
</div>

[sect4]
<div class="sect4{style? {style}}{role? {role}}">
<h5{id? id="{id}"}>{title}</h5>
|
</div>

[appendix]
<div class="sect1{style? {style}}{role? {role}}">
<h2{id? id="{id}"}>{numbered?{sectnum} }{appendix-caption} {counter:appendix-number:A}: {title}</h2>
<div class="sectionbody">
|
</div>
</div>

[toc]
<div id="toc">
  <div id="toctitle">{toc-title}</div>
  <noscript><p><b>JavaScript must be enabled in your browser to display the table of contents.</b></p></noscript>
</div>

[header]
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="{quirks=application/xhtml+xml}{quirks?text/html}; charset={encoding}" />
<meta name="description" content="{description}" />
<meta name="keywords" content="{keywords}" />
<title>GenomeTools - Tools</title>
{title%}<title>GenomeTools - Tools</title>
<link rel="stylesheet" type="text/css" href="style.css">
<link rel="stylesheet" href="{stylesdir=.}/{stylesheet}" type="text/css" />
</head>
<body>
<div id="menu">
<ul>
<li><a href="index.html">Overview</a></li>
<li><a href="pub/">Download</a></li>
<li><a href="https://github.com/genometools/genometools">Browse source</a></li>
<li><a href="http://github.com/genometools/genometools/issues/">Issue tracker</a></li>
<li><a href="documentation.html">Documentation</a></li>
  <ul class="submenu">
    <li><a id="current" href="tools.html">Tools</a></li>
    <li><a href="manuals.html">Manuals</a></li>
    <li><a href="libgenometools.html">C API</a></li>
    <li><a href="docs.html"><tt>gtscript</tt> docs</a></li>
    <li><a href="contract.html">Development Contract</a></li>
    <li><a href="contribute.html">Contribute</a></li>
  </ul>
<li><a href="annotationsketch.html"><tt>AnnotationSketch</tt></a></li>
<li><a href="/cgi-bin/gff3validator.cgi">GFF3 validator</a></li>
<li><a href="license.html">License</a></li>
</ul>
</div>
<div id="main">
<h1> GenomeTools Tools </h1>
<p>This list shows all <em>GenomeTools</em> tools and their functions.</p>


[footer]
<div id="footer">
Copyright &copy; 2007-2016 The <i>GenomeTools</i> authors.
</div>
</div>
<!-- Piwik -->
<script type="text/javascript">
var pkBaseURL = "https://zenlicensemanager.com/piwik/";
document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
</script><script type="text/javascript">
try {
var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 5);
piwikTracker.trackPageView();
piwikTracker.enableLinkTracking();
} catch( err ) {}
</script><noscript><p><img src="https://zenlicensemanager.com/piwik/piwik.php?idsite=5" style="border:0" alt="" /></p></noscript>
<!-- End Piwik Tracking Tag -->
</body>
</html>

[oldftr]
</div>
{disable-javascript%<div id="footnotes"><hr /></div>}
<div id="footer">
<div id="footer-text">
template::[footer-text]
</div>
ifdef::badges[]
<div id="footer-badges">
ifndef::icons[]
Valid <a href="http://validator.w3.org/check?uri=referer">XHTML</a>
and <a href="http://jigsaw.w3.org/css-validator/check/referer">CSS</a>.
endif::icons[]
ifdef::icons[]
<a href="http://validator.w3.org/check?uri=referer">
  <img style="border:0;width:88px;height:31px"
    src="http://www.w3.org/Icons/valid-xhtml11-blue"
    alt="Valid XHTML 1.1" height="31" width="88" />
</a>
<a href="http://jigsaw.w3.org/css-validator/">
  <img style="border:0;width:88px;height:31px"
    src="http://jigsaw.w3.org/css-validator/images/vcss-blue"
    alt="Valid CSS!" />
</a>
endif::icons[]
</div>
endif::badges[]
</div>
</body>
</html>

ifdef::doctype-manpage[]
[synopsis]
template::[sect1]
endif::doctype-manpage[]

ifdef::quirks[]
include::xhtml11-quirks.conf[]
endif::quirks[]
