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comparison slopBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
1 <tool id="bedtools_slopbed" name="SlopBed" 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 bedtools slop
11 $pct
12 $strand
13 -g $genome
14 -i $inputA
15 #if $addition.addition_select == 'b':
16 -b $addition.b
17 #else:
18 -l $addition.l
19 -r $addition.r
20 #end if
21 $header
22 > $output
23 ]]>
24 </command>
25 <inputs>
26 <param format="bed,vcf,gff,gff3" name="inputA" 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="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
34 <expand macro="addition" />
35 <expand macro="print_header" />
36 </inputs>
37 <outputs>
38 <data format="bed" name="output"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="inputA" value="a.bed" ftype="bed" />
43 <param name="genome" value="mm9_chr1.len" ftype="bed" />
44 <param name="addition_select" value="b" />
45 <param name="b" value="5" />
46 <output name="output" file="slopBed_result1.bed" ftype="bed" />
47 </test>
48 <test>
49 <param name="inputA" value="a.bed" ftype="bed" />
50 <param name="genome" value="mm9_chr1.len" ftype="bed" />
51 <param name="addition_select" value="lr" />
52 <param name="l" value="2" />
53 <param name="r" value="3" />
54 <output name="output" file="slopBed_result2.bed" ftype="bed" />
55 </test>
56 </tests>
57 <help>
58 <![CDATA[
59 **What it does**
60
61 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
62
63 .. image:: $PATH_TO_IMAGES/slop-glyph.png
64
65 .. class:: warningmark
66
67 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
68 @REFERENCES@
69 ]]>
70 </help>
71 <expand macro="citations" />
72 </tool>