annotate data_manager/genomad_datamanager.xml @ 3:34b729713d0c draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_genomad commit fea5692fe5258a520e43b739c5aa4d109756123f

<?xml version="1.0"?>
<tool id="genomad_build_database" name="geNomad" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.11.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <requirement type="package" version="1.21.4">wget</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        set -eo pipefail; 
        wget -O - 
            ## #if $version == "test"
            ##     https://zenodo.org/records/11945948/files/genomad_microdb.tar.gz?download=1
            ## #else
                https://portal.nersc.gov/genomad/__data__/genomad_db_v${version}.tar.gz
                ## alternatively https://zenodo.org/records/14886553, but constructing the links is more complicated
            ## #end if
        | tar -xzv &&
        mkdir -p '$out_file.extra_files_path' &&
        mv genomad_db '$out_file.extra_files_path' &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "genomad":[
      {
        "path":"genomad_db",
        "name":"Version $version",
        "value":"$version"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="version" type="select" multiple="false" label="Database Version" help="Download the chosen version from https://portal.nersc.gov/genomad/__data__/">
            <option value="1.7">1.7</option>
            <option value="1.9">1.9</option>
            <!-- <option value="test">test</option> -->
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="version" value="1.9" />
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"1.9"'/>
                    <has_text text='"name":"Version 1.9"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Download and extract geNomad database from https://portal.nersc.gov/genomad/__data__/

Check for tool and DB version compatibility here: https://portal.nersc.gov/genomad/__data__/releases.txt
    ]]></help>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>