<tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '${out_file.extra_files_path}' &&
        #if $type == "test"
            touch '${out_file.extra_files_path}'/empty
        #else
            SemiBin download_GTDB --reference-db-data-dir '${out_file.extra_files_path}'
        #end if
        && cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[#slurp
#from datetime import datetime
#set value=datetime.now().strftime("%d%m%Y")
{
  "data_tables":{
    "gtdb":[
      {
        "value": "$value",
#if $type == "test"
        "name": "Test",
        "dbkey": "test",
#else
        "name": "GTDB reference genome generated by MMseqs2 used in SemiBin",
        "dbkey": "gtdb",
#end if
        "path": "$out_file.extra_files_path"
      }
    ]
  }
}
]]></configfile>
    </configfiles>
    <inputs>
        <param name="type" type="hidden" value="" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
    <test expect_num_outputs="1">
        <param name="type" value="test" />
        <output name="out_file">
            <assert_contents>
                <has_text text="test"/>
                <has_text text="Test"/>
            </assert_contents>
        </output>
    </test>
    </tests>
    <help><![CDATA[
This tool downloads reference genomes (GTDB) for SemiBin
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41467-022-29843-y</citation>
    </citations>
</tool>