view data_manager/eukcc.xml @ 0:7f11e0da0e4f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3

<tool id="data_manager_eukcc" name="EukCC data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <macros>
        <token name="@TOOL_VERSION@">2.1.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">eukcc</requirement>
    </requirements>
    <version_command>eukcc --version | cut -d" " -f3</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir '$output_file.extra_files_path' &&
        wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_${version}.tar.gz &&
        tar -xvf eukcc2_db_ver_${version}.tar.gz &&
        rm eukcc2_db_ver_${version}.tar.gz &&
        mv eukcc2_db_ver_${version}/* '$output_file.extra_files_path'/ &&
        cp '$dmjson' '$output_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
    {
      "data_tables":{
        "eukcc":[
          {
            "value":"$version",
            "name":"EukCC DB ${version}",
            "version":"${version}",
            "path":"$output_file.extra_files_path"
          }
        ]
      }
    }]]></configfile>
    </configfiles>
    <inputs>
        <param name="version" type="select" label="DB version">
            <option value="1.2">1.2</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- data to large for test in CI
        <test>
            <param name="version" value="1.2"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="EukCC DB"/>
                    <has_text text="1.2"/>
                    <has_text text="eukcc"/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[
        This data managers fetches EukCC reference data from http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/
    ]]></help>
    <citations>
        <citation type="doi">10.1186/s13059-020-02155-4</citation>
    </citations>
</tool>