Mercurial > repos > xuebing > sharplabtool

comparison mytools/bedsort.xml @ 7:f0dc65e7f6c0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:59:07 -0500
parents
children
comparison
equal deleted inserted replaced
6:094f377db4e5 7:f0dc65e7f6c0
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>