Mercurial > repos > dereeper > beagle
comparison execute_beagle.xml @ 0:a929ef8dea25 draft default tip
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author | dereeper |
---|---|
date | Tue, 14 Aug 2018 07:59:19 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:a929ef8dea25 |
---|---|
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> |