|
0
|
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 > $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>
|
