Mercurial > repos > iuc > bedtools

comparison flankBed.xml @ 1:82aac94b06c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents
children 607c0576c6ab
comparison
equal deleted inserted replaced
0:b8348686a0b9 1:82aac94b06c3
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 <![CDATA[
10 flankBed
11 $pct
12 $strand
13 -g $genome
14 -i $input
15
16 #if $addition.addition_select == 'b':
17 -b $addition.b
18 #else:
19 -l $addition.l
20 -r $addition.r
21 #end if
22 > $output
23 ]]>
24 </command>
25 <inputs>
26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
27 <expand macro="genome" />
28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
29 label="Define -l and -r as a fraction of the feature’s length"
30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
32 label="Define -l and -r based on strand"
33 help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
34 <expand macro="addition" />
35 </inputs>
36 <outputs>
37 <data metadata_source="input" format_source="input" name="output" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="input" value="a.bed" ftype="bed" />
42 <param name="genome" value="mm9_chr1.len"/>
43 <param name="addition_select" value="b"/>
44 <param name="b" value="5"/>
45 <output name="output" file="flankBed_result1.bed" ftype="bed" />
46 </test>
47 <test>
48 <param name="input" value="a.bed" ftype="bed" />
49 <param name="genome" value="mm9_chr1.len"/>
50 <param name="addition_select" value="lr"/>
51 <param name="l" value="2"/>
52 <param name="r" value="3"/>
53 <output name="output" file="flankBed_result2.bed" ftype="bed" />
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58 **What it does**
59
60 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
61
62 .. image:: $PATH_TO_IMAGES/flank-glyph.png
63
64 .. class:: warningmark
65
66 In order to prevent creating intervals that violate chromosome boundaries, bedtools flank requires a genome file defining the length of each chromosome or contig.
67
68 @REFERENCES@
69 ]]>
70 </help>
71 <expand macro="citations" />
72 </tool>