# HG changeset patch
# User iuc
# Date 1652108845 0
# Node ID d9b0eda57c0b8cc24008b586edb7ac03697731bd
# Parent  0f45b98a5a0803c3eb7a2c7ffa199b13f9d174bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt commit 6bde7c9985265b3086f1e1a6df814c20d02ee092"

diff -r 0f45b98a5a08 -r d9b0eda57c0b macros.xml
--- a/macros.xml	Fri Nov 12 18:38:49 2021 +0000
+++ b/macros.xml	Mon May 09 15:07:25 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.5.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">
         <requirements>
diff -r 0f45b98a5a08 -r d9b0eda57c0b malt_run.xml
--- a/malt_run.xml	Fri Nov 12 18:38:49 2021 +0000
+++ b/malt_run.xml	Mon May 09 15:07:25 2022 +0000
@@ -7,9 +7,6 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 
-## This will point to a directory.
-#set ref = str($reference.fields.path)
-
 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
 ## malt-run uses the file extension to determine the input format.
 #if $input.is_of_type('fasta', 'fasta.gz'):
@@ -42,7 +39,7 @@
 
 --alignmentType '$alignmentType'
 --inFile '$input_identifier'
---index '$ref'
+--index '$reference.fields.path'
 ## malt-run requires correct output file extensions.
 --output './output.rma6'
 --numThreads \${GALAXY_SLOTS:-12}