# HG changeset patch
# User iuc
# Date 1726990007 0
# Node ID 54a6fb045aea7fcf961fe689c03a6daf9258f824
# Parent  ac3bae00a3500bd27dd2a95f0f1512832d452e02
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain commit 303002db06287fb25306020c4391626842f52162

diff -r ac3bae00a350 -r 54a6fb045aea axtchain.xml
--- a/axtchain.xml	Mon Aug 26 17:34:26 2024 +0000
+++ b/axtchain.xml	Sun Sep 22 07:26:47 2024 +0000
@@ -3,7 +3,7 @@
         Chain together axt alignments
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">455</token>
+        <token name="@TOOL_VERSION@">469</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
@@ -70,7 +70,7 @@
     <help><![CDATA[
 **What it does**
 
-`axtChain`_ is a tool to chain together alignments. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
+`axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
 
 
 sample linearGap file (loose)::
@@ -82,9 +82,12 @@
     tGap    325     360     400     450     600     1100    3600    7600    15600   31600   56600
     bothGap 625     660     700     750     900     1400    4000    8000    16000   32000   57000
 
+For implementation details see axtChain's `source code`_.
 
 .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
+.. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtChain/axtChain.c
     ]]>    </help>
     <citations>
         <citation type="doi">10.1093/bib/bbs038</citation>