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planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author dereeper
date Tue, 14 Aug 2018 07:59:19 -0400
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1 <tool id="Beagle" name="Beagle" version="1.0.0" >
2 <description>Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection</description>
3 <requirements>
4 <requirement type="package" version="4.0">Beagle</requirement>
5 </requirements>
6 <command interpreter="bash">$__tool_directory__/execute_beagle.sh $vcf_input $phase $impute</command>
7 <inputs>
8 <param format="vcf" name="vcf_input" type="data" label="Variant call format"/>
9 <param type="text" name="phase" value="5" help="Non-negative integer" label="specifies the number of iterations for estimating genotype phase (default: phase-its=5).Increasing this parameter will typicall increase genotype phaseaccuracy."/>
10 <param type="text" name="impute" value="5" help="Non-negative integer" label="specifies the number of iterations for estimating genotypes at ungenotyped markers (default:impute-its=5). Increasing this parameter (up to ~10 iterations) will typically increase genotype imputation accuracy."/>
11 </inputs>
12 <outputs>
13 <data format="vcf" name="vcf_ouput" label="Phased and imputed VCF" from_work_dir="out.vcf"/>
14 <data format="txt" name="log" label="Beagle log file" from_work_dir="out.log"/>
15 </outputs>
16
17 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
18 <tests>
19 <!-- [HELP] Test files have to be in the ~/test-data directory -->
20 <test>
21 <param name="vcf_input" value="Annotated_VCF.vcf" />
22 <param name="phase" value="5" />
23 <param name="impute" value="5" />
24 <output name="vcf_ouput" file="output.vcf" compare="sim_size"/>
25 <output name="log" file="filelog.txt" compare="sim_size"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29
30
31
32 .. class:: infomark
33
34 **Beagle** version 4
35 | **If you use Beagle in a published analysis, please report the program version and cite the following article** "S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-97."
36
37 .. class:: infomark
38
39 **Galaxy integration** Provided by Southgreen & Marcon Valentin (IFB & INRA)
40
41 .. class:: infomark
42
43 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
44
45 ---------------------------------------------------
46
47 ======
48 Beagle
49 ======
50
51 -----------
52 Description
53 -----------
54
55 | Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
56
57 Version 4 has multiple improvements:
58
59 a standard format (Variant Call Format) for input and output files
60 a powerful identity by descent detection algorithm: Refined IBD
61 support for multi-threaded computation
62 support for multi-allelic markers
63 improved methods for phasing and genotype imputation
64 elimination of temporary files
65 use of a sliding window permit control memory use
66
67 | For further informations, please visite the Beagle website_.
68
69
70 .. _website: https://faculty.washington.edu/browning/beagle/b4_0.html
71
72
73 ]]></help>
74 <citations>
75 <citation type="doi">10.1086/521987</citation>
76 </citations>
77
78 </tool>