src/hg/htdocs/goldenPath/help/customTrack.html d88300025cbc54935141d132c49336b8d7768ac7

d88300025cbc54935141d132c49336b8d7768ac7
jnavarr5
  Mon May 6 16:09:04 2024 -0700
Adding a table of contents to the Custom Track help page. Moving all examples to the bottom of the page. Adding summarys to some steps. Reorganizing text to be in a more digestable manor. Fixing broken links to the file formats page. Making all titles sentence case, refs #19736

diff --git src/hg/htdocs/goldenPath/help/customTrack.html src/hg/htdocs/goldenPath/help/customTrack.html
index 8327d48..e08e905 100755
--- src/hg/htdocs/goldenPath/help/customTrack.html
+++ src/hg/htdocs/goldenPath/help/customTrack.html
@@ -1,37 +1,40 @@
 <!DOCTYPE html>
 <!--#set var="TITLE" value="Genome Browser Custom Tracks" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!-- Relative paths to support mirror sites with non-standard GB docs install -->
 <!--#include virtual="$ROOT/inc/gbPageStart.html" -->
 
 <h1>Displaying Your Own Annotations in the Genome Browser</h1>
 <h2>Table of Contents</h2>
 <ul>
   <li><a href="#CustomTracks">What are custom annotation tracks?</a></li>
     <ul>
       <li><a href="#CREATE">Building and sharing a custom track</a></li>
-      <li><a href="#EXAMPLE1">Example #1: Simple annotation file</a></li>
-      <li><a href="#EXAMPLE2">Example #2: Two annotations track in one file</a></li>
-      <li><a href="#EXAMPLE3a">Example #3a: BED example with multiple blocks</a></li>
-      <li><a href="#EXAMPLE3b">Example #3b: Simple annotation in bigBed format</a></li>
-      <li><a href="#EXAMPLE4">Example #4: URL substitution using the 'name' field</a></li>
     </ul>
   <li><a href="#ADD_CT">Loading a custom track into the Genome Browser</a></li>
   <li><a href="#MANAGE">Displaying and managing custom tracks</a></li>
     <ul>
-      <li><a href="#BROWSER">Creating Browser lines for annotations</a></li>
+      <li><a href="#BROWSER">Creating browser lines for annotations</a></li>
+      <li><a href="#BROWSERextra">Additional browser line options</a></li>
       <li><a href="#TRACK">Defining track lines for annotations</a></li>
+      <li><a href="#PAIRS">Required and useful track attribute pairs</a></li>
     </ul>
   <li><a href="#SHARE">Sharing your annotation track with others</a></li>
-    <ul>
-      <li><a href="#EXAMPLE5">Example #5: Loading a custom track via the URL</a></li>
-      <li><a href="#EXAMPLE6">Example #6: Constructing a URL using the bigDataUrl setting</a></li>
-    </ul>
   <li><a href="#TROUBLE">Troubleshooting annotation display problems</a></li>
 </ul>
+  <h6>Custom Track Examples:</h6>
+    <ul>
+      <li><a href="#EXAMPLE1">Simple annotation file</a></li>
+      <li><a href="#EXAMPLE2">Two annotations track in one file</a></li>
+      <li><a href="#EXAMPLE3a">BED custom track with multiple blocks</a></li>
+      <li><a href="#EXAMPLE3b">Simple annotation in bigBed format</a></li>
+      <li><a href="#EXAMPLE4">Create external links using the 'name' field from the BED file</a></li>
+      <li><a href="#EXAMPLE5">Loading a custom track via the URL</a></li>
+      <li><a href="#EXAMPLE6">Construct a sharable URL using the bigDataUrl setting</a></li>
+    </ul>
 <!--#include virtual="customTrackText.html"-->
 
 <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->