# HG changeset patch
# User iuc
# Date 1695723015 0
# Node ID 4e8120950f5d6da5c63cadbe021f4d310e84d976
# Parent  f31e3eb599ba5e27c241bed7e2b2fa8b8fae49a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58

diff -r f31e3eb599ba -r 4e8120950f5d macros.xml
--- a/macros.xml	Wed Oct 12 07:40:44 2022 +0000
+++ b/macros.xml	Tue Sep 26 10:10:15 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.7.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="bio_tools">
         <xrefs>
@@ -37,10 +37,10 @@
             #if $reference_source.ref_file.ext.endswith(".gz")
                 gunzip -c '$reference_source.ref_file' > reference.fa &&
             #else
-                ln -f -s '$reference_source.ref_file' reference.fa &&
+                cp '$reference_source.ref_file' reference.fa &&
             #end if
         #else:
-            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+            cp '$reference_source.ref_file.fields.path' reference.fa &&
         #end if
     ]]></token>
 
diff -r f31e3eb599ba -r 4e8120950f5d snp.xml
--- a/snp.xml	Wed Oct 12 07:40:44 2022 +0000
+++ b/snp.xml	Tue Sep 26 10:10:15 2023 +0000
@@ -140,6 +140,7 @@
 This module decodes probabilities to SNPs but NOT indels.
 
 For a more general solution see the medaka *variant* tool.
+
 ----
 
 .. class:: infomark