# HG changeset patch
# User iuc
# Date 1617048339 0
# Node ID 43815fa60f3ad101b02b8bed255237b4427f6dc1
# Parent  edf6d4003fadbf3884713a667c4ebc8d9b3f246e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"

diff -r edf6d4003fad -r 43815fa60f3a macros.xml
--- a/macros.xml	Tue Feb 23 20:13:39 2021 +0000
+++ b/macros.xml	Mon Mar 29 20:05:39 2021 +0000
@@ -29,7 +29,11 @@
 
     <token name="@REF_FASTA@"><![CDATA[
         #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' reference.fa &&
+            #if $reference_source.ref_file.ext.endswith(".gz")
+                gunzip -c '$reference_source.ref_file' > reference.fa &&
+            #else
+                ln -f -s '$reference_source.ref_file' reference.fa &&
+            #end if
         #else:
             ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
         #end if
@@ -85,7 +89,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
+                <param name="ref_file" type="data" format="fasta,fasta.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
             </when>
         </conditional>
     </xml>
diff -r edf6d4003fad -r 43815fa60f3a test-data/ref.fasta.gz
Binary file test-data/ref.fasta.gz has changed
diff -r edf6d4003fad -r 43815fa60f3a variant.xml
--- a/variant.xml	Tue Feb 23 20:13:39 2021 +0000
+++ b/variant.xml	Mon Mar 29 20:05:39 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy6" profile="@PROFILE@">
+<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy7" profile="@PROFILE@">
     <description>Probability decoding</description>
     <macros>
         <import>macros.xml</import>
@@ -166,7 +166,7 @@
             </conditional>
             <conditional name="reference_source">
                 <param name="reference_source_selector" value="history"/>
-                <param name="ref_file" value="ref.fasta"/>
+                <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/>
             </conditional>
             <conditional name="output_annotated">
                 <param name="output_annotated_select" value="true"/>