view data_manager/checkm2_datamanager.xml @ 1:64630d815957 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7

<tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <!-- on update run a local test setting `test` to something else than "true" -->
        <token name="@TOOL_VERSION@">1.0.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">23.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
    </requirements>
    <version_command>checkm2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path' &&
        #if $test != "true"
            checkm2 database --download --path  '$out_file.extra_files_path'/ &&
            mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
        #else
            touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
        #end if
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "checkm2":[
      {
        "path":"uniref100.KO.1.dmnd",
        "dbkey":"@TOOL_VERSION@",
        "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
        "version":"@TOOL_VERSION@",
        "value":"@TOOL_VERSION@"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="test" type="hidden"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="test" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"@TOOL_VERSION@"'/>
                    <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Download and extract CheckM2 reference data.
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41592-023-01940-w</citation>
    </citations>
</tool>