# HG changeset patch
# User iuc
# Date 1631478945 0
# Node ID 8dfe8a52346f8866ab142558187bad3b521539f3
# Parent  1ca4ce7241fd52810e47a05758099f49ac7b20ad
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"

diff -r 1ca4ce7241fd -r 8dfe8a52346f macros.xml
--- a/macros.xml	Thu Apr 22 20:25:13 2021 +0000
+++ b/macros.xml	Sun Sep 12 20:35:45 2021 +0000
@@ -2,6 +2,11 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.2</token>
     <token name="@PROFILE@">20.01</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">khmer</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
@@ -109,4 +114,4 @@
     <token name="@REFERENCES@"><![CDATA[
 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
     ]]></token>
-</macros>
\ No newline at end of file
+</macros>
diff -r 1ca4ce7241fd -r 8dfe8a52346f medaka_consensus.xml
--- a/medaka_consensus.xml	Thu Apr 22 20:25:13 2021 +0000
+++ b/medaka_consensus.xml	Sun Sep 12 20:35:45 2021 +0000
@@ -6,6 +6,7 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
+ln -s '$d' 'input_assembly.fa' &&
 medaka_consensus
 ## optional
 -m ${m}
@@ -14,7 +15,7 @@
 -t \${GALAXY_SLOTS:-4}
 ## required
 -i '$i'
--d '$d'
+-d 'input_assembly.fa'
 
 2>&1 | tee '$out_log'
     ]]></command>