diff macros.xml @ 3:a6318f87f2cd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00

--- a/macros.xml	Thu Sep 07 05:29:24 2023 +0000
+++ b/macros.xml	Thu Feb 15 15:47:19 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.2.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
@@ -75,7 +75,7 @@
     <token name="@input_reference@"><![CDATA[
         #if $tool.reference_genome.source == 'history':
             #set $ref_genome = 'reference.fasta'
-            ln -s -f '${tool.reference_genome.history_item}' $ref_genome &&
+            ln -s -f '${tool.reference_genome.history_item}' '$ref_genome' &&
         #else:
             #set $ref_genome = $tool.reference_genome.index.fields.path
         #end if
@@ -83,9 +83,7 @@
     <token name="@input_annotation_double@"><![CDATA[
         #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext)
         #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext)
-        ln -s '${tool.input_annotation1}' $input1 &&
-        ln -s '${tool.input_annotation2}' $input2 &&
+        ln -s '${tool.input_annotation1}' '$input1' &&
+        ln -s '${tool.input_annotation2}' '$input2' &&
     ]]></token>
-    
-
 </macros>