<tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0">
    <description>use intervals to mask sequences from a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools maskfasta
            $soft
            -mc '${mc}'
            -fi '${fasta}'
            -bed '${input}'
            -fo '${output}'
            $fullheader
]]>
    </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 name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue=""
            label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
            help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" />
        <param name="mc" type="text"  value="N"
            label="Replace masking character"
            help="That is, instead of masking with Ns, use another character. (-mc)" />
        <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue=""
            label="Use full fasta header." 
            help="By default, only the word before the first space or tab is used"/>
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="soft" value="False" />
            <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="soft" value="True" />
            <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.

.. image:: $PATH_TO_IMAGES/maskfasta-glyph.png

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