annotate data_manager/checkv_datamanager.xml @ 2:88042a5ead89 draft

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

<tool id="checkv_build_database" name="CheckV" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.3</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <!-- DM only needs diamon (which comes with checkv) -->
        <requirement type="package" version="@TOOL_VERSION@">checkv</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        set -eo pipefail; 
        wget https://portal.nersc.gov/CheckV/checkv-db-v${version}.tar.gz &&
        tar -zxvf checkv-db-v${version}.tar.gz &&
        cd checkv-db-v${version}/genome_db/ &&
        diamond makedb --in checkv_reps.faa --db checkv_reps &&
        cd - &&
        mkdir -p '$out_file.extra_files_path' &&
        mv checkv-db-v${version} '$out_file.extra_files_path'/checkv-db &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "checkv":[
      {
        "path":"checkv-db/",
        "name":"Version $version",
        "version":"$version",
        "value":"$version"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="version" type="select" multiple="false" label="Database Version">
            <option value="1.5">1.5</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <!-- <test expect_num_outputs="1">
            <param name="version" value="1.5" />
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"1.5"'/>
                    <has_text text='"name":"Version 1.5"'/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[
Download and extract CheckV reference data from https://portal.nersc.gov/CheckV/
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-020-00774-7</citation>
    </citations>
</tool>