# HG changeset patch
# User iuc
# Date 1656351031 0
# Node ID cb34f00cc10f559549b700298145e927fa2bef63
# Parent  72b5e9dda577e33bedecd8ec01066eda28f5b96b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054

diff -r 72b5e9dda577 -r cb34f00cc10f macros.xml
--- a/macros.xml	Thu Nov 18 20:01:28 2021 +0000
+++ b/macros.xml	Mon Jun 27 17:30:31 2022 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.4.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">20.01</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">21.01</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">medaka</xref>
@@ -166,6 +166,6 @@
     ]]></token>
 
     <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>`_.
+More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_.
     ]]></token>
 </macros>
diff -r 72b5e9dda577 -r cb34f00cc10f medaka_consensus.xml
--- a/medaka_consensus.xml	Thu Nov 18 20:01:28 2021 +0000
+++ b/medaka_consensus.xml	Mon Jun 27 17:30:31 2022 +0000
@@ -6,7 +6,8 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-ln -s '$d' 'input_assembly.fa' &&
+## symlink seems insuffiencient (fai file is still created next to link target)
+cp '$d' 'input_assembly.fa' &&
 medaka_consensus
 ## optional
 -m ${m}
@@ -125,7 +126,7 @@
 
 **Input**
 
-An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these.
+An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://github.com/nanoporetech/medaka/blob/master/docs/walkthrough.rst>`_ for a detailed example of one method of obtaining these.
 
 ----