# HG changeset patch
# User richard-burhans
# Date 1724096543 0
# Node ID 1aee697ec0fcf913258fb356089cff55e9987805
# Parent  ae309acc76e8749c170074450bf7c10fbbc81672
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 899fc661e76905ace1a27aad1563b62e01944ce7

diff -r ae309acc76e8 -r 1aee697ec0fc batched_lastz.xml
--- a/batched_lastz.xml	Fri Aug 16 15:45:50 2024 +0000
+++ b/batched_lastz.xml	Mon Aug 19 19:42:23 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="batched_lastz" name="Batched Lastz" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="batched_lastz" name="Batched LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>: align batches of sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -17,7 +17,7 @@
         <param argument="--input" type="data" format="tgz" label="Tarball"/>
     </inputs>
     <outputs>
-        <data name="output" label="Batched Lastz on ${on_string}" format="auto" />
+        <data name="output" label="Batched LASTZ on ${on_string}" format="auto" />
     </outputs>
     <tests>
       <test expect_num_outputs="1">
@@ -26,7 +26,19 @@
       </test>
     </tests>
     <help><![CDATA[
-    Run batched lastz
+Batched LASTZ is a special version of LASTZ designed to process output of Galaxy's SegAlign tool. It outputs pairiwse alignments in a verietry of formats.
+
+**Using this tool**
+
+.. class:: warningmark
+
+This tool is the second part of a two-step process for generation of paiwrise alignments. The output of this tool is alignments in a format that was specified in **Output Options** section of SegAlign tool.
+
+**What it does**
+
+SegAlign processes **Target** and **Query** sequences to identify highly similar regions where gapped extension will be performed to create actual alignments. The actual alignments are generated by **Batched LASTZ** that should be run on the output of this tool. 
+
+The default output is a MAF alignment file. Other formats can be configured in *Output Options* section.  See LASTZ manual <https://lastz.github.io/lastz/#formats>`_ for description of possible formats.
     ]]></help>
     <expand macro="citations"/>
 </tool>