<tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools links
            -base "${basename}"
            -org "${org}"
            -db "${db}"
            -i "${input}"
            > "${output}"
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
        <param name="basename" type="text" value="http://genome.ucsc.edu"
            label="The 'basename' for the UCSC genome browser" />
        <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
        <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
    </inputs>
    <outputs>
        <data name="output" format="html" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="linksBed1.bed" ftype="bed" />
            <param name="basename" value="http://genome.ucsc.edu" />
            <param name="org" value="" />
            <param name="db" value="" />
            <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
        </test>
        <test>
            <param name="input" value="linksBed1.bed" ftype="bed" />
            <param name="basename" value="http://genome.ucsc.edu" />
            <param name="org" value="mouse" />
            <param name="db" value="mm9" />
            <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.

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