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1 <tool id="closestbed" name="closestBed">
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2 <description>find closest features</description>
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3 <command>closestBed -a $inputa -b $inputb $strandness -d $no -t $tie> $output_data
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4 </command>
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5 <inputs>
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6 <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/>
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7 <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/>
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8 <param name="strandness" type="select" label="Strand requirement" >
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9 <option value="" selected="true"> none </option>
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10 <option value="-s" > -s: closest feature on the same strand</option>
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11 <option value="-S" > -S: closest feature on the opposite strand </option>
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12 </param>
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13
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14 <param name="no" label="Only look for non-overlaping features" type="boolean" truevalue="-no" falsevalue="" checked="False"/>
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15 <param name="tie" type="select" label="Strand requirement" >
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16 <option value="all" selected="true"> report all ties </option>
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17 <option value="first" > report the first that occurred</option>
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18 <option value="last" > report the last that occurred </option>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="input" name="output_data"/>
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23 </outputs>
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24 <help>
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25
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26 **What it does**
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27
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28 This is a wrapper for closestBed.
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29
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30 </help>
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31 </tool>
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32
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