view data_manager/vibrant_datamanager.xml @ 1:3f68072f2da6 draft

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

<tool id="vibrant_build_database" name="vibrant" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">VIBRANT</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">vibrant</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        set -eo pipefail; 
        mkdir -p '$out_file.extra_files_path'/vibrant_db &&
        download-db.sh '$out_file.extra_files_path'/vibrant_db &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{
  "data_tables":{
    "vibrant":[
      {
        "path":"vibrant_db",
        "name":"Version @TOOL_VERSION@",
        "version":"@TOOL_VERSION@",
        "value":"@TOOL_VERSION@"
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs/>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <!-- <test expect_num_outputs="1">
            <output name="out_file">
                <assert_contents>
                    <has_text text='"value":"@TOOL_VERSION@"'/>
                    <has_text text='"name":"Version @TOOL_VERSION@"'/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[
Download and vibrant reference data using https://raw.githubusercontent.com/AnantharamanLab/VIBRANT/master/databases/VIBRANT_setup.py
    ]]></help>
    <citations>
        <citation type="doi">10.1186/s40168-020-00867-0</citation>
    </citations>
</tool>