Mercurial > repos > xuebing > sharplabtool
diff bedsort.xml @ 11:b7f1d9f8f3bc
Uploaded
author | xuebing |
---|---|
date | Sat, 10 Mar 2012 07:59:27 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedsort.xml Sat Mar 10 07:59:27 2012 -0500 @@ -0,0 +1,23 @@ +<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>