<tool id="zinbra" name="Zinbra" version="0.0.1">
    <description>ChIP-Seq enrichment</description>
    <requirements>
        <requirement type="package" version="0.0.1">epigenome</requirement>
    </requirements>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <command interpreter="python">
        zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
    </command>
    <inputs>
        <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" />
        <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" />
    </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>