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author devteam
date Thu, 19 Mar 2015 14:40:35 -0400
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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3">
2 <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio" />
8 <command>
9
10 #if str($analysis_type) == "count":
11 vcfhetcount "${vcf_input}" > "${out_file1}"
12 #elif str($analysis_type) == "ratio":
13 vcfhethomratio "${vcf_input}" > "${out_file1}"
14 #elif str($analysis_type) == "allele_count":
15 vcfcountalleles "${vcf_input}" > "${out_file1}"
16 #end if
17
18 </command>
19
20 <inputs>
21 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
22 <option value="count">Compute the number of heterozygotes</option>
23 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
24 <option value="allele_count">Compute the total number of alleles</option>
25 </param>
26 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
27 </inputs>
28 <outputs>
29 <data format="tabular" name="out_file1" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="analysis_type" value="count"/>
34 <param name="vcf_input" value="vcflib.vcf"/>
35 <output name="out_file1" file="vcfhethom-test1.tab"/>
36 </test>
37 <test>
38 <param name="analysis_type" value="ratio"/>
39 <param name="vcf_input" value="vcflib.vcf"/>
40 <output name="out_file1" file="vcfhethom-test2.tab"/>
41 </test>
42 <test>
43 <param name="analysis_type" value="allele_count"/>
44 <param name="vcf_input" value="vcflib.vcf"/>
45 <output name="out_file1" file="vcfhethom-test3.tab"/>
46 </test>
47 </tests>
48 <help>
49
50 This tool performs three basic calculations:
51
52 (1) Computes the number of heterozygotes
53 (2) Computes the ratio between heterozygotes and homozygotes
54 (3) Computes the total number of alleles in the input dataset
55
56 ----
57
58 This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
59
60 </help>
61 <expand macro="citations" />
62 </tool>