Mercurial > repos > xuebing > sharplabtool
view tools/mytools/bedsort.xml @ 3:33c067c3ae34
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author | xuebing |
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date | Fri, 09 Mar 2012 19:47:53 -0500 |
parents | 9071e359b9a3 |
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<tool id="bedsort" name="sort"> <description>a interval file by chr and start</description> <command> head -n $skip $input > $output && tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output </command> <inputs> <param name="input" type="data" format="bed" label="Input interval file"/> <param name="skip" type="integer" value="0" label="top lines to skip" help="output directly, not sorted"/> </inputs> <outputs> <data format="bed" name="output" /> </outputs> <help> **Description** Unix command used:: head -n $skip $input > $output tail -n+`expr $skip + 1` $input | sort -k1,1 -k2,2g >> $output </help> </tool>