# HG changeset patch
# User iuc
# Date 1624643136 0
# Node ID 09b53c1d4ab1f5639064804e5b1873abb08df467
# Parent  1f06dccdc5d1503b9c76887a82f6648553fd885f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"

diff -r 1f06dccdc5d1 -r 09b53c1d4ab1 macros.xml
--- a/macros.xml	Fri Jun 11 21:40:01 2021 +0000
+++ b/macros.xml	Fri Jun 25 17:45:36 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.20</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy1</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy2</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>
diff -r 1f06dccdc5d1 -r 09b53c1d4ab1 minimap2.xml
--- a/minimap2.xml	Fri Jun 11 21:40:01 2021 +0000
+++ b/minimap2.xml	Fri Jun 25 17:45:36 2021 +0000
@@ -131,7 +131,7 @@
     $io_options.L
     $io_options.c
     #if $io_options.cs:
-        --cs $io_options.cs
+        --cs=$io_options.cs
     #end if
     $io_options.Y
     #if $io_options.K:
@@ -470,6 +470,11 @@
                 <param name="z" value="400" />
                 <param name="s" value="40" />
             </section>
+            <section name="io_options">
+                <!-- the next setting is a noop for bam output, but tests that
+                a valid command line is formed for the cs option -->
+                <param name="cs" value="none" />
+            </section>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>        
         <test>