view data_manager/iphop_datamanager.xml @ 2:d636e6221f8e draft

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

<tool id="iphop_build_database" name="iPHoP" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.3</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">iphop</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path'/db &&
        iphop download
            --db_dir '$out_file.extra_files_path'/db
            --db_version $db_version
            ## --full_verify  https://bitbucket.org/srouxjgi/iphop/issues/114/db-download-verification-error
            --no_prompt &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "iphop":[
      {
        "path":"db",
        "name":"Version $db_version",
        "version":"$db_version",
        "value":"$db_version"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="db_version" type="select" multiple="false" label="Database Version">
            <option value="iPHoP_db_Aug23_rw">iPHoP_db_Aug23_rw</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <!-- <test expect_num_outputs="1">
            <param name="db_version" value="iPHoP_db_Aug23_rw" />
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"iPHoP_db_Aug23_rw"'/>
                    <has_text text='"name":"Version iPHoP_db_Aug23_rw"'/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[
Download and extract iPHoP reference data
    ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pbio.3002083</citation>
    </citations>
</tool>