annotate bed_resize.xml @ 0:9b9b4c24eb34

Uploaded
author xuebing
date Sat, 31 Mar 2012 13:19:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
1 <tool id="bed_resize" name="bed_resize">
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
2 <description>change interval size</description>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">bed_resize.py $infile $outfile $expr_start $expr_end $strand </command>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
4 <inputs>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
5 <param name="infile" format="interval" type="data" label="Original file"/>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
6 <param name="expr_start" size="20" type="text" value="start-0" label="start=" help="e.g. start+10, start-10, end-100"/>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
7 <param name="expr_end" size="20" type="text" value="end+0" label="end=" help="e.g. end-100, start+10"/>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
8 <param name="strand" label="Enforce strandness" type="boolean" truevalue="strand" falsevalue="ignore" checked="False"/>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
9 </inputs>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
10 <outputs>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
11 <data format="input" name="outfile" />
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
12 </outputs>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
13 <help>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
14
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
15 **What it does**
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
16
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
17 This tool changes start and end of each row in an interval file. When strandness is enforced, chromosome start and end are treated as the 5' and 3' end for intervals on the '+' strand, and the opposite for intervals on the '-' strand. In the expression such as 'start=start-1000', 'start' and 'end' are interpreted as the 5' and 3' end, respectively, and the operator '+' and '-' means moving downsteam and upsteam, respectively. For example, when enforcing strandness,
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
18
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
19 **start=start-1000**: extend 1000 bp on the 5' end (moving start upstream)
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
20
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
21 **start=start+1000**: trancate 1000 bp on the 5' end (moving start downsteam)
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
22
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
23 **end=end+1000**: extend 1000 bp on the 3' end (moving end downsteam)
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
24
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
25 **end=start+1000**: moving the end to 1000 bp downsteam of the start (return the first 1000 bp on the 5' end)
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
26
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
27 **end=start+1**: taking the 5' end of the interval
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
28
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
29 **start=end-1**: taking the 3' end of the interval
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
30
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
31 </help>
9b9b4c24eb34 Uploaded
xuebing
parents:
diff changeset
32 </tool>