<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>calculate Fisher statistic between two feature files</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools fisher
$strand
$split
-a '$inputA'
-b '$inputB'
@OVERLAP@
-g @GENOME_FILE@
$reciprocal
$m
> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="input_conditional_genome_file" />
        <expand macro="strand2" />
        <expand macro="split" />
        <expand macro="overlap" />
        <expand macro="reciprocal" />
        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false"
            label="Merge overlapping intervals before looking at overlap" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="fisherBed1.bed" ftype="bed" />
            <param name="inputB" value="fisherBed2.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="fisherBed.len" ftype="tabular" />
            <output name="output" file="fisherBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.

@REFERENCES@
    ]]></help>
    <expand macro="citations" />
</tool>