diff data_manager/data_manager_defense_finder.xml @ 3:46528ab18f85 draft

planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/data_managers/data_manager_defense_finder commit 3fd15f07b1a8750245e5748aedf33d5d407f2ae5-dirty

--- a/data_manager/data_manager_defense_finder.xml	Thu Feb 13 14:36:45 2025 +0000
+++ b/data_manager/data_manager_defense_finder.xml	Fri May 02 11:11:35 2025 +0000
@@ -1,29 +1,48 @@
-<tool id="defense_finder_models_fetcher_data_manager" name="DefenseFinder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0">
-    <description>genotype data fetcher</description>
-    <macros>
-        <token name="@TOOL_VERSION@">2.0.0</token>
-    </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">defense-finder</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/defense_finder_models_fetcher.py' --out '${out_file}' --version '${model_version}'
+<tool id="defense_finder_models_fetcher_data_manager" name="DefenseFinder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy1" profile="21.05">
+  <description>DefenseFinder models fetcher</description>
+  <macros>
+    <token name="@TOOL_VERSION@">2.0.0</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">defense-finder</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        defense-finder update --models-dir '$out_file.extra_files_path'/'defense-finder-models_$model_version' &&
+        cp '$dmjson' '$out_file'
     ]]></command>
-    <inputs>
-        <param name="model_version" type="text" label="Defense finder models version" help="The available versions can be found at : https://github.com/mdmparis/defense-finder-models/releases"/>
-        <param name="software_compatibility" type="text" label="List of defenseFinder versions compatibility" help="Enter the list of defenseFinder software versions that are compatible with the current model (e.g., 1.2.0,1.3.0,2.0.0). Separate multiple versions with commas if required."/>
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="model_version" value="2.0.2"/>
-            <param name="software_compatibility" value="2.0.0"/>
-            <output name="out_file" value="defense_finder_test_data_manager.json"/>
-        </test>
-    </tests>
-    <help><![CDATA[
+  <configfiles>
+    <configfile name="dmjson">{
+  "data_tables": {
+    "defense-finder-2": [
+      {
+        "value": "defense-finder-models_$model_version",
+        "dbkey": "defense-finder-models",
+        "version": "$model_version",
+        "name": "version $model_version",
+        "description": "MacSyFinder models allowing for a systematic search of anti-phage systems",
+        "path": "defense-finder-models_$model_version",
+        "compatibility_version": "$software_compatibility"
+      }
+    ]
+  }
+}</configfile>
+  </configfiles>
+  <inputs>
+    <param name="model_version" type="text" label="Defense finder models version" help="The available versions can be found at : https://github.com/mdmparis/defense-finder-models/releases"/>
+    <param name="software_compatibility" type="text" label="List of defenseFinder versions compatibility" help="Enter the list of defenseFinder software versions that are compatible with the current model (e.g., 1.2.0,1.3.0,2.0.0). Separate multiple versions with commas if required."/>
+  </inputs>
+  <outputs>
+    <data name="out_file" format="data_manager_json"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="model_version" value="2.0.2"/>
+      <param name="software_compatibility" value="2.0.0"/>
+      <output name="out_file" value="defense_finder_test_data_manager.json"/>
+    </test>
+  </tests>
+  <help><![CDATA[
 Download Defense Finder models : https://github.com/mdmparis/defense-finder-models/
 check out the defense finder models versions from https://github.com/mdmparis/defense-finder-models/releases
 
@@ -31,9 +50,9 @@
 Starting from models version 2.0.0, only DefenseFinder version 2.0.0 is comaptible.
 
 
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1038/s41467-022-30269-9</citation>
-        <citation type="doi">10.24072/pcjournal.250</citation>
-    </citations>
+    ]]>  </help>
+  <citations>
+    <citation type="doi">10.1038/s41467-022-30269-9</citation>
+    <citation type="doi">10.24072/pcjournal.250</citation>
+  </citations>
 </tool>