<tool id="zinbra" name="Zinbra" version="0.0.1">
    <description>ChIP-Seq analysis</description>
    <requirements>
        <requirement type="package" version="0.0.1">integration_jar</requirement>
    </requirements>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:"/>
        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
        #if $action.selection == "analyze"
            zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
        #else
            zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
        #end if
    </command>
    <inputs>
        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
        <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
        <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
        <conditional name="action">
            <param name="selection" type="select" label="Action">
                <option value="analyze">Compute enrichment of ChIP-Seq</option>
                <option value="compare">Compare different ChIP-Seqs</option>
            </param>
            <when value="analyze">
                <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/>
            </when>
            <when value="compare">
                <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/>
                <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="result" format="bed" label="result.bed"/>
    </outputs>
    <help>
Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.
https://github.com/JetBrains-Research/zinbra
    </help>
</tool>