<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.1">
    <description>profile the nucleotide content of intervals in a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools nuc
        $s
        $seq
        #if str($pattern):
            -pattern '$pattern'
            $C
        #end if
        -fi '$fasta'
        -bed '$input'
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
        <param format="fasta" name="fasta" type="data" label="FASTA file"/>

        <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
            label="Profile the sequence according to strand" />
        <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
            label="Print the extracted sequence" />
        <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
            <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
        </param>
        <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue=""
            label="Ignore case when matching -pattern"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <output name="output" file="nucBed_result1.bed" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="seq" value="True" />
            <output name="output" file="nucBed_result2.bed" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="seq" value="True" />
            <param name="pattern" value="TAC" />
            <output name="output" file="nucBed_result3.bed" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Profiles the nucleotide content of intervals in a fasta file.

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