|
0
|
1 <tool id="vcftools_slice" name="Slice VCF" version="0.1">
|
|
|
2 <description>to get data from selected regions</description>
|
|
|
3
|
|
|
4 <requirements>
|
|
|
5 <requirement type="binary">echo</requirement>
|
|
|
6 <requirement type="package" version="0.1.11">vcftools</requirement>
|
|
|
7 </requirements>
|
|
|
8
|
|
|
9 <command>
|
|
|
10 ## Only works if input is sorted.
|
|
|
11 vcf-sort ${input} > sorted.vcf
|
|
|
12
|
|
|
13 ## As of v0.1.10, the first line of a BED file is assumed to be a header and ignored,
|
|
|
14 ## so add a dummy header line if necessary.
|
|
|
15 #set first_line = open( str($regions) ).readline()
|
|
|
16 #if first_line.startswith( '#' ):
|
|
|
17 ## Header already exists, so just link.
|
|
|
18 ; ln -s $regions regions.bed
|
|
|
19 #else:
|
|
|
20 ## Add dummy header.
|
|
|
21 ; echo '#dummy header' | cat - $regions > regions.bed
|
|
|
22 #end if
|
|
|
23
|
|
|
24 ## Slice VCF.
|
|
|
25 ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode
|
|
|
26 </command>
|
|
|
27
|
|
|
28 <inputs>
|
|
|
29 <param name="input" label="Input dataset" type="data" format="vcf"/>
|
|
|
30 <param name="regions" label="Regions" type="data" format="bed"/>
|
|
|
31 </inputs>
|
|
|
32
|
|
|
33 <outputs>
|
|
|
34 <data name="output" format="vcf" from_work_dir="output.recode.vcf"/>
|
|
|
35 </outputs>
|
|
|
36
|
|
|
37 <tests>
|
|
|
38 <test>
|
|
|
39 <param name="input" value="slice_in.vcf"/>
|
|
|
40 <param name="regions" value="regions.bed"/>
|
|
|
41 <output name="output" file="slice_out.vcf"/>
|
|
|
42 </test>
|
|
|
43 </tests>
|
|
|
44
|
|
|
45 <help>
|
|
|
46 Please see the VCFtools `documentation`__ for help and further information.
|
|
|
47
|
|
|
48 .. __: http://vcftools.sourceforge.net/docs.html
|
|
|
49 </help>
|
|
|
50 </tool>
|
