<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
    <description>calculate Fisher statistic between two feature files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools fisher
        $strand
        $split
        -a '$inputA'
        -b '$inputB'
        -f $overlap
        -g @GENOME_FILE@
        $reciprocal
        $m
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
        <expand macro="input_conditional_genome_file" />
        <expand macro="strand2" />
        <expand macro="split" />
        <expand macro="overlap" />
        <expand macro="reciprocal" />
        <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
            label="Merge overlapping intervals before looking at overlap" help="(-m)" />
    </inputs>
    <outputs>
        <data name="output" metadata_source="inputA" format_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>