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1 <?xml version="1.0"?>
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2
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3 <tool id="extend_bed_regions_1" name="Expand or contract regions">
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4 <description>in a BED file by a fixed number of bases</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">extend_bed_regions $in_bed $extent $strand $out_bed</command>
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7 <inputs>
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8 <param format="bed" name="in_bed" type="data" label="BED file whose regions should be modified"/>
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9 <param name="extent" type="integer" value="50" label="Number of bases to extend each BED region (negative values cause contraction)"/>
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10 <param name="strand" type="select" display="radio" label="Which end to extend?" help="If the BED file contains strand info, extension will be strand specific. Otherwise, the positive strand is assumed">
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11 <option value="5">5'</option>
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12 <option value="3">3'</option>
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13 <option value="both" selected="true">Both</option>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data name="out_bed" format="bed" type="data" label="BED file with extended/contracted regions"/>
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18 </outputs>
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19
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20 <tests/>
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21
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22 <help>
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23 This tool expands each regions defined in a BED file by the specified amount, at the specified end(s). If expanded regions overlap, they are merged.
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24 </help>
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25
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26 </tool>
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