annotate data_manager/data_manager_defense_finder.xml @ 4:502208b90cfe draft default tip

planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/data_managers/data_manager_defense_finder commit b775193cea6a19a591981c9f8540c5c059b1e1ea

<tool id="defense_finder_models_fetcher_data_manager" name="DefenseFinder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy2" 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' '$out_file'
    ]]></command>
  <configfiles>
    <configfile name="dmjson">{
  "data_tables": {
    "defense-finder-2": [
      {
        "value": "defense-finder-models_$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",
        "soft_compatibility_version": "$soft_compatibility_version"
      }
    ]
  }
}</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="soft_compatibility_version" 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="soft_compatibility_version" 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


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>
</tool>