From b7238a092a9bfb37e670c6c380c3985e048bae9a Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2025 13:14:55 +0100
Subject: [PATCH] Adjust test tool and datatype config to best practices
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Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 test/functional/tools/create_directory_index.xml | 4 ++--
 test/functional/tools/sample_datatypes_conf.xml  | 2 +-
 test/functional/tools/use_directory_index.xml    | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/functional/tools/create_directory_index.xml b/test/functional/tools/create_directory_index.xml
index 9de2448947dd..3c849f238fed 100644
--- a/test/functional/tools/create_directory_index.xml
+++ b/test/functional/tools/create_directory_index.xml
@@ -1,7 +1,7 @@
 <tool id="create_directory_index" name="Create directory index" version="1.0" profile="24.2">
     <command><![CDATA[
 mkdir '$index.extra_files_path' &&
-cp '$reference' '$index.extra_files_path'/1.fasta
+cp '$reference' '$index.extra_files_path/1.fasta'
     ]]></command>
     <inputs>
         <param name="reference" type="data" label="Select a genome to index" help="Build an index for this FASTA sequence." format="fasta"/>
@@ -12,7 +12,7 @@ cp '$reference' '$index.extra_files_path'/1.fasta
     <tests>
         <test>
             <param name="reference" value="1.fasta"></param>
-            <output name="index">
+            <output name="index" ftype="bwa_mem2_index">
                 <extra_files name="1.fasta" type="file" value="1.fasta"></extra_files>
             </output>
         </test>
diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml
index 6e0c724e9a59..534d35122ec9 100644
--- a/test/functional/tools/sample_datatypes_conf.xml
+++ b/test/functional/tools/sample_datatypes_conf.xml
@@ -60,7 +60,7 @@
     </datatype>
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
-    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory"/>
+    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>
     <datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
   </registration>
 </datatypes>
diff --git a/test/functional/tools/use_directory_index.xml b/test/functional/tools/use_directory_index.xml
index f415f09a6374..f4c2aaddf54f 100644
--- a/test/functional/tools/use_directory_index.xml
+++ b/test/functional/tools/use_directory_index.xml
@@ -1,6 +1,6 @@
 <tool id="use_directory_index" name="Uses directory index" version="1.0" profile="24.2">
     <command><![CDATA[
-cp '$reference.extra_files_path'/1.fasta '$output'
+cp '$reference.extra_files_path/1.fasta' '$output'
     ]]></command>
     <inputs>
         <param name="reference" type="data" label="Select an index" format="bwa_mem2_index"/>