<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>reports the distances between features</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools spacing
-i '$input'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" metadata_source="input" label="Spaces between intervals of ${input}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <output name="output" file="spacingBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Report the spacing between intervals in a file.

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