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comparison vcftools_subset.xml @ 0:23436d1d0fa1 draft default tip

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author devteam
date Sun, 24 Nov 2013 17:13:57 -0500
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1 <tool id="vcftools_subset" name="Subset" version="0.1">
2 <description>columns from a VCF dataset</description>
3
4 <requirements>
5 <requirement type="package">tabix</requirement>
6 <requirement type="package" version="0.1.11">vcftools</requirement>
7 </requirements>
8
9 <command>
10 ln -s ${input} input.vcf ;
11
12 ## Sort file.
13 sort -k1,1 -k2,2n input.vcf > input.vcf.sorted ;
14
15 ## Compress.
16 bgzip input.vcf.sorted ;
17
18 ## Index.
19 tabix -p vcf input.vcf.sorted.gz ;
20
21 ## Subset.
22 vcf-subset ${trim_alt_alleles} ${exclude_rows_with_no_variants} -c "${columns}" input.vcf.sorted.gz > $output
23 </command>
24
25 <inputs>
26 <param name="input" label="Input dataset" type="data" format="vcf"/>
27 <param name="columns" label="Columns" type="text" value=""/>
28 <param name="trim_alt_alleles" type="select" label="Remove alternate alleles if not found in the subset" help="">
29 <option value="" selected="True">No</option>
30 <option value="-a">Yes</option>
31 </param>
32 <param name="exclude_rows_with_no_variants" type="select" label="Exclude rows not containing variants" help="">
33 <option value="" selected="True">No</option>
34 <option value="-e">Yes</option>
35 </param>
36 </inputs>
37
38 <outputs>
39 <data name="output" format="vcf"/>
40 </outputs>
41
42 <stdio>
43 <regex match=".*" source="both" level="log" description="tool progress"/>
44 </stdio>
45
46 <tests>
47 <test>
48 <param name="input" value="subset_in.vcf"/>
49 <param name="columns" value="sample1"/>
50 <param name="trim_alt_alleles" value="Yes"/>
51 <param name="exclude_rows_with_no_variants" value="Yes"/>
52 <!-- 2 lines diff because command line with full file path is included in output VCF, and
53 it not possible to match full file path. -->
54 <output name="output" file="subset_out.vcf" lines_diff="2"/>
55 </test>
56 </tests>
57
58 <help>
59 Please see the VCFtools `documentation`__ for help and further information.
60
61 .. __: http://vcftools.sourceforge.net/docs.html
62 </help>
63 </tool>