Mercurial > repos > dereeper > beagle
annotate execute_beagle.xml @ 0:a929ef8dea25 draft default tip
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date | Tue, 14 Aug 2018 07:59:19 -0400 |
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1 <tool id="Beagle" name="Beagle" version="1.0.0" > |
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2 <description>Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection</description> |
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3 <requirements> |
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4 <requirement type="package" version="4.0">Beagle</requirement> |
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5 </requirements> |
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6 <command interpreter="bash">$__tool_directory__/execute_beagle.sh $vcf_input $phase $impute</command> |
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7 <inputs> |
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8 <param format="vcf" name="vcf_input" type="data" label="Variant call format"/> |
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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."/> |
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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."/> |
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11 </inputs> |
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12 <outputs> |
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13 <data format="vcf" name="vcf_ouput" label="Phased and imputed VCF" from_work_dir="out.vcf"/> |
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14 <data format="txt" name="log" label="Beagle log file" from_work_dir="out.log"/> |
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15 </outputs> |
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16 |
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17 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> |
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18 <tests> |
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19 <!-- [HELP] Test files have to be in the ~/test-data directory --> |
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20 <test> |
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21 <param name="vcf_input" value="Annotated_VCF.vcf" /> |
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22 <param name="phase" value="5" /> |
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23 <param name="impute" value="5" /> |
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24 <output name="vcf_ouput" file="output.vcf" compare="sim_size"/> |
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25 <output name="log" file="filelog.txt" compare="sim_size"/> |
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26 </test> |
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27 </tests> |
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28 <help><![CDATA[ |
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29 |
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30 |
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31 |
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32 .. class:: infomark |
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33 |
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34 **Beagle** version 4 |
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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." |
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36 |
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37 .. class:: infomark |
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38 |
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39 **Galaxy integration** Provided by Southgreen & Marcon Valentin (IFB & INRA) |
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40 |
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41 .. class:: infomark |
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42 |
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43 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
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44 |
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45 --------------------------------------------------- |
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46 |
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47 ====== |
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48 Beagle |
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49 ====== |
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50 |
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51 ----------- |
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52 Description |
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53 ----------- |
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54 |
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55 | Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. |
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56 |
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57 Version 4 has multiple improvements: |
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58 |
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59 a standard format (Variant Call Format) for input and output files |
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60 a powerful identity by descent detection algorithm: Refined IBD |
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61 support for multi-threaded computation |
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62 support for multi-allelic markers |
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63 improved methods for phasing and genotype imputation |
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64 elimination of temporary files |
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65 use of a sliding window permit control memory use |
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66 |
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67 | For further informations, please visite the Beagle website_. |
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68 |
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69 |
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70 .. _website: https://faculty.washington.edu/browning/beagle/b4_0.html |
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71 |
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72 |
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73 ]]></help> |
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74 <citations> |
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75 <citation type="doi">10.1086/521987</citation> |
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76 </citations> |
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77 |
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78 </tool> |