<tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.0.1+galaxy0" python_template_version="3.5">
    <description>converts aplcms HDF output to RamClustR csv input</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="1.1.5">pandas</requirement>
        <requirement type="package" version="3.6.1">pytables</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${hdf_dataframe}' --table '${table_name}' '${out_file}'
    ]]></command>
    <inputs>
        <param name="hdf_dataframe" type="data" format="h5" label="apLCMS Dataset"/>
        <param name="table_name" type="select" label="Table Name">
            <option value="peaks">peaks</option>
            <option value="aligned_peaks">aligned peaks</option>
        </param>
    </inputs>
    <outputs>
        <data format="csv" name="out_file" label="CSV with ${table_name} from ${hdf_dataframe.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="hdf_dataframe" value="test-input.h5" ftype="h5"/>
            <param name="table_name" value="peaks"/>
            <output name="out_file" file="test-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/aplcms>`_  Unsupervised or Hybrid

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