diff data_manager/busco_fetcher.xml @ 4:171e112d2030 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30

--- a/data_manager/busco_fetcher.xml	Mon Apr 24 12:26:36 2023 +0000
+++ b/data_manager/busco_fetcher.xml	Thu Feb 20 20:14:32 2025 +0000
@@ -1,19 +1,34 @@
 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
     <description>dataset dowloader</description>
         <macros>
-        <token name="@TOOL_VERSION@">5.4.6</token>
+        <token name="@TOOL_VERSION@">5.8.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/data_manager.py'
-            --database '$lineage'
-            --name $lineage+\$(date +'%Y-%m-%d-%H%M%S')
-            --json '$out_file'
-            --version '@TOOL_VERSION@'
+        mkdir '$out_file.extra_files_path' &&
+        busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
+        cp '$dmjson' '$out_file' 
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import datetime
+    {
+      "data_tables":{
+        "busco_database":[
+          {
+            "value":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
+            "name":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
+            "version":"@TOOL_VERSION@",
+            "path":"$out_file.extra_files_path"
+          }
+        ]
+      }
+    }]]>
+            </configfile>
+        </configfiles>
     <inputs>
         <param name="lineage" type="select" label="Select the lineage to be downloaded">
             <option value="all">All</option>
@@ -31,7 +46,7 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text="virus"/>
-                    <has_text text="5.4.6"/>
+                    <has_text text="5.8.0"/>
                 </assert_contents>
             </output>
         </test>