<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@">
    <description>create a HTML page of links to UCSC locations</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 name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
            label="The 'basename' for the UCSC genome browser" />
        <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
        <param argument="-db" type="text" value="hg19" label="The genome build" />
    </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>