--- a/data_manager/data_manager_semibin.xml	Fri Oct 14 21:32:55 2022 +0000
+++ b/data_manager/data_manager_semibin.xml	Fri Aug 01 21:25:02 2025 +0000
@@ -1,18 +1,45 @@
 <tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">24.0</token>
+    </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
     </requirements>
-    <macros>
-        <token name="@TOOL_VERSION@">1.1.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@PROFILE@">21.01</token>
-    </macros>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/data_manager_semibin.py'
-    --json '$out_file'
-    $type
+        mkdir -p '${out_file.extra_files_path}' &&
+        #if $type == "test"
+            touch '${out_file.extra_files_path}'/empty
+        #else
+            SemiBin download_GTDB --reference-db-data-dir '${out_file.extra_files_path}'
+        #end if
+        && cp '$dmjson' '$out_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#from datetime import datetime
+#set value=datetime.now().strftime("%d%m%Y")
+{
+  "data_tables":{
+    "gtdb":[
+      {
+        "value": "$value",
+#if $type == "test"
+        "name": "Test",
+        "dbkey": "test",
+#else
+        "name": "GTDB reference genome generated by MMseqs2 used in SemiBin",
+        "dbkey": "gtdb",
+#end if
+        "path": "$out_file.extra_files_path"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="type" type="hidden" value="" />
     </inputs>
@@ -21,7 +48,7 @@
     </outputs>
     <tests>
     <test expect_num_outputs="1">
-        <param name="type" value="--test" />
+        <param name="type" value="test" />
         <output name="out_file">
             <assert_contents>
                 <has_text text="test"/>