<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools nuc
        $strand
        $seq
        $pattern
        $case
        -fi $fasta 
        -bed $inputA
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param format="fasta" name="fasta" type="data" label="Fasta file"/>

        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." />
        <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." />
        <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" label="Report the number of times a user-defined sequence is observed (case-sensitive)." />
        <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." />
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <help>

**What it does**

Profiles the nucleotide content of intervals in a fasta file.

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