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1 <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 linksBed
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10 -base $basename
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11 -org $org
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12 -db $db
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13 -i $inputA
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14 > $output
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15 </command>
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16 <inputs>
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17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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18 <param name="basename" type="text" value="http://genome.ucsc.edu" label="The “basename” for the UCSC browser" />
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19 <param name="org" type="text" value="human" label="The organism (e.g. mouse, human)" />
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20 <param name="db" type="text" value="hg18" label="The genome build" />
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="html" />
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24 </outputs>
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25 <help>
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26
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27 **What it does**
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28
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29 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.
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30
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31 @REFERENCES@
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32 </help>
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33 </tool>
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