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1 <tool id="bedsort" name="sort">
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2 <description>a interval file by chr and start</description>
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3 <command> head -n $skip $input > $output
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4 && tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="bed" label="Input interval file"/>
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8 <param name="skip" type="integer" value="0" label="top lines to skip" help="output directly, not sorted"/>
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9 </inputs>
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10 <outputs>
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11 <data format="bed" name="output" />
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12 </outputs>
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13 <help>
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14
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15 **Description**
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16
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17 Unix command used::
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18
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19 head -n $skip $input > $output
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20 tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output
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21
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22 </help>
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23 </tool>
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