view data_manager/phabox_datamanager.xml @ 1:334bd61d216d draft

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_phabox commit c78bd5eafa3d9450305cc8b32ba9cf8c64c42ba7

<tool id="phabox_build_database" name="PhaBOX" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">2.1.5</token>
        <token name="@DB_VERSION@">2</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <requirement type="package" version="6.0">unzip</requirement>
        <requirement type="package" version="1.21.4">wget</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v@DB_VERSION@.zip &&
        unzip phabox_db_v@DB_VERSION@.zip &&
        mkdir -p '$out_file.extra_files_path' &&
        mv "phabox_db_v@DB_VERSION@" '$out_file.extra_files_path' &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "phabox":[
      {
        "path":"phabox_db_v@DB_VERSION@",
        "name":"Version @DB_VERSION@",
        "version":"@DB_VERSION@",
        "value":"@DB_VERSION@"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs/>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"@DB_VERSION@"'/>
                    <has_text text='"name":"Version 2'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Download and extract PhaBOX reference data. The current tool version is used for versioning. For the user only the major version is shown
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioadv/vbad101</citation>
    </citations>
</tool>