Mercurial > repos > iuc > bedtools

comparison flankbed.xml @ 0:4fb5ea02b441 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
parents
children 7511823bdea1
comparison
equal deleted inserted replaced
-1:000000000000 0:4fb5ea02b441
1 <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 flankBed
10 $pct
11 $strand
12 -g $genome
13 -i $inputA
14
15 #if $addition.addition_select == 'b':
16 -b $addition.b
17 #else:
18 -l $addition.l
19 -r $addition.r
20 #end if
21
22 &gt; $output
23 </command>
24 <inputs>
25 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
26 <expand macro="genome" />
27 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
28 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
29 <expand macro="addition" />
30 </inputs>
31 <outputs>
32 <data format="bed" name="output" label=""/>
33 </outputs>
34 <help>
35
36 **What it does**
37
38 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
39
40 .. image:: $PATH_TO_IMAGES/flank-glyph.png
41
42 .. class:: warningmark
43
44 In order to prevent creating intervals that violate chromosome boundaries, bedtools flank requires a genome file defining the length of each chromosome or contig.
45
46 @REFERENCES@
47 </help>
48 </tool>