<tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0">
    <description>remove intervals based on overlaps</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools subtract
        $strand
        -a $inputA
        -b $inputB
        -f $overlap
        $removeIfOverlap
        > $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="strand2" />
        <expand macro="overlap" />
        <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
            <option value="" selected="True">Dont Remove entire feature on overlap</option>
            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option>
            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option>
        </param>
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
            <output name="output" file="subtractBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
            <param name="overlap" value="0.80" />
            <output name="output" file="subtractBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
            <param name="removeIfOverlap" value="-A" />
            <output name="output" file="subtractBed_result3.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.

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

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