<tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.1.0+galaxy0" python_template_version="3.5">
    <description>converts apLCMS parquet output to RamClustR csv input</description>
    <requirements>
        <requirement type="package" version="1.1.5">pandas</requirement>
        <requirement type="package" version="4.0.0">pyarrow</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${aplcms_dataframe}' '${out_file}'
    ]]></command>
    <inputs>
        <param name="aplcms_dataframe" type="data" format="parquet" label="apLCMS Dataframe"/>
    </inputs>
    <outputs>
        <data format="csv" name="out_file" label="Feature-by-sample ${aplcms_dataframe.name} table (csv)"/>
    </outputs>
    <tests>
        <test>
            <param name="aplcms_dataframe" value="input.parquet" ftype="parquet"/>
            <output name="out_file" file="output.csv" ftype="csv"/>
        </test>
    </tests>
    <help><![CDATA[
        Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.

        **Workflow position**

        - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms>`_  Unsupervised or Hybrid

        - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
    ]]></help>
</tool>