<tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>profile the nucleotide content of intervals in a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
ln -s '$fasta' 'input.fasta' &&
bedtools nuc
$s
$seq
#if str($pattern):
    -pattern '$pattern'
    $C
#end if
-fi 'input.fasta'
-bed '$input'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>

        <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
            label="Profile the sequence according to strand" />
        <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
            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" truevalue="-C" falsevalue="" checked="false"
            label="Ignore case when matching -pattern"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </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>