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author | dereeper |
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date | Tue, 14 Aug 2018 07:59:19 -0400 |
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<tool id="Beagle" name="Beagle" version="1.0.0" > <description>Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection</description> <requirements> <requirement type="package" version="4.0">Beagle</requirement> </requirements> <command interpreter="bash">$__tool_directory__/execute_beagle.sh $vcf_input $phase $impute</command> <inputs> <param format="vcf" name="vcf_input" type="data" label="Variant call format"/> <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."/> <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."/> </inputs> <outputs> <data format="vcf" name="vcf_ouput" label="Phased and imputed VCF" from_work_dir="out.vcf"/> <data format="txt" name="log" label="Beagle log file" from_work_dir="out.log"/> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="vcf_input" value="Annotated_VCF.vcf" /> <param name="phase" value="5" /> <param name="impute" value="5" /> <output name="vcf_ouput" file="output.vcf" compare="sim_size"/> <output name="log" file="filelog.txt" compare="sim_size"/> </test> </tests> <help><![CDATA[ .. class:: infomark **Beagle** version 4 | **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." .. class:: infomark **Galaxy integration** Provided by Southgreen & Marcon Valentin (IFB & INRA) .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- ====== Beagle ====== ----------- Description ----------- | Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Version 4 has multiple improvements: a standard format (Variant Call Format) for input and output files a powerful identity by descent detection algorithm: Refined IBD support for multi-threaded computation support for multi-allelic markers improved methods for phasing and genotype imputation elimination of temporary files use of a sliding window permit control memory use | For further informations, please visite the Beagle website_. .. _website: https://faculty.washington.edu/browning/beagle/b4_0.html ]]></help> <citations> <citation type="doi">10.1086/521987</citation> </citations> </tool>