Mercurial > repos > xuebing > sharplabtool
comparison bedsort.xml @ 11:b7f1d9f8f3bc
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author | xuebing |
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date | Sat, 10 Mar 2012 07:59:27 -0500 |
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10:1558594a3c2e | 11:b7f1d9f8f3bc |
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1 <tool id="bedsort" name="sort"> | |
2 <description>a interval file by chr and start</description> | |
3 <command> head -n $skip $input > $output | |
4 && 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> |