Mercurial > repos > anton > vcfhethom
annotate vcfhethom.xml @ 2:efba18d7b34b
Updated tool version to 0.0.2
author | Anton Nekrutenko <anton@bx.psu.edu> |
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date | Wed, 25 Jun 2014 16:49:42 -0400 |
parents | 41099cdfe806 |
children | 5731e8c3ffde |
rev | line source |
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2
efba18d7b34b
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
1
diff
changeset
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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.2"> |
0 | 2 <requirements> |
1
41099cdfe806
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
|
3 <requirement type="package" version="86723982aa">vcflib</requirement> |
0 | 4 </requirements> |
5 <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description> | |
6 <command> | |
7 | |
8 #if str($analysis_type) == "count": | |
9 vcfhetcount "${vcf_input}" > "${out_file1}" | |
10 #elif str($analysis_type) == "ratio": | |
11 vcfhethomratio "${vcf_input}" > "${out_file1}" | |
12 #elif str($analysis_type) == "allele_count": | |
13 vcfcountalleles "${vcf_input}" > "${out_file1}" | |
14 #end if | |
15 | |
16 </command> | |
17 | |
18 <inputs> | |
19 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:"> | |
20 <option value="count">Compute the number of heterozygotes</option> | |
21 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option> | |
22 <option value="allele_count">Compute the total number of alleles</option> | |
23 </param> | |
24 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/> | |
25 </inputs> | |
26 <outputs> | |
27 <data format="tabular" name="out_file1" /> | |
28 </outputs> | |
29 <tests> | |
30 <test> | |
31 <param name="analysis_type" value="count"/> | |
32 <param name="vcf_input" value="vcflib.vcf"/> | |
33 <output name="out_file1" file="vcfhethom-test1.tab"/> | |
34 </test> | |
35 <test> | |
36 <param name="analysis_type" value="ratio"/> | |
37 <param name="vcf_input" value="vcflib.vcf"/> | |
38 <output name="out_file1" file="vcfhethom-test2.tab"/> | |
39 </test> | |
40 <test> | |
41 <param name="analysis_type" value="allele_count"/> | |
42 <param name="vcf_input" value="vcflib.vcf"/> | |
43 <output name="out_file1" file="vcfhethom-test3.tab"/> | |
44 </test> | |
45 </tests> | |
46 <help> | |
47 | |
48 This tool performs three basic calculations: | |
49 | |
50 (1) Computes the number of heterozygotes | |
51 (2) Computes the ratio between heterozygotes and homozygotes | |
52 (3) Computes the total number of alleles in the input dataset | |
53 | |
54 ---- | |
55 | |
56 This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
57 | |
58 </help> | |
59 </tool> |