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comparison mytools/bedsort.xml @ 9:87eb5c5ddfe9

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author xuebing
date Fri, 09 Mar 2012 20:01:43 -0500
parents f0dc65e7f6c0
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8:361ec1c0479d 9:87eb5c5ddfe9
1 <tool id="bedsort" name="sort">
2 <description>a interval file by chr and start</description>
3 <command> head -n $skip $input > $output
4 &amp;&amp; tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output
5 </command>
6 <inputs>
7 <param name="input" type="data" format="bed" label="Input interval file"/>
8 <param name="skip" type="integer" value="0" label="top lines to skip" help="output directly, not sorted"/>
9 </inputs>
10 <outputs>
11 <data format="bed" name="output" />
12 </outputs>
13 <help>
14
15 **Description**
16
17 Unix command used::
18
19 head -n $skip $input > $output
20 tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output
21
22 </help>
23 </tool>