annotate linksBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

<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>
        linksBed
        -base $basename
        -org $org
        -db $db
        -i $inputA
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param name="basename" type="text" value="http://genome.ucsc.edu" label="The “basename” for the UCSC browser" />
        <param name="org" type="text" value="human" label="The organism (e.g. mouse, human)" />
        <param name="db" type="text" value="hg18" label="The genome build" />
    </inputs>
    <outputs>
        <data name="output" format="html" />
    </outputs>
    <help>

**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>