<tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0">
    <requirements>
        <requirement type="package" version="7.0">click</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file'
    ]]></command>
    <inputs>
       <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/>
       <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/>
       <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/>
    </inputs>
    <outputs>
        <data name="output_file" format_source="input_file"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="deseq2_peaks.bed"/>
            <output name="output_file" value="grouped.bed"/>
        </test>
    </tests>
    <help><![CDATA[
Can be used to get the lowest p.adj for 2 consecutive peaks in a gene.
The reported p.adj is the higher p.adj of the 2 consecutive peaks.
    ]]></help>
</tool>