<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>converter</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bed12ToBed6
-i '$input'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED12 file to BED6"/>
    </inputs>
    <outputs>
        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED6)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bed12.bed" ftype="bed" />
            <output name="output" file="bed12ToBed6_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bed12ToBed6 is a convenience tool that converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).

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