<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>remove intervals based on overlaps</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools subtract
$strand
-a '$inputA'
-b '$inputB'
@OVERLAP@
$removeIfOverlap
> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="strand2" />
        <expand macro="overlap" />
        <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
            <option value="" selected="true">Don't 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 (-A)</option>
            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature) (-N)</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" 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>