Mercurial > repos > dereeper > admixture
comparison admixture.xml @ 0:781ac6e7a3a1 draft
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| author | dereeper |
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| date | Fri, 20 Feb 2015 10:09:18 -0500 |
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| -1:000000000000 | 0:781ac6e7a3a1 |
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| 1 <tool id="admixture" name="Admixture" version="1.23"> | |
| 2 <description>a population structure from large SNP genotype datasets</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.07">plink</requirement> | |
| 5 <requirement type="package" version="1.23">admixture</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="bash">./admixture.sh $input $outputs $logs $best_k_output $best_k_logfile $kmin $kmax | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> | |
| 11 <param type="text" name="kmin" label="K min" value="1"/> | |
| 12 <param type="text" name="kmax" label="K max" value="5"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="txt" name="best_k_output" label="Best K Output"/> | |
| 16 <data format="txt" name="best_k_logfile" label="Best K Logfile"/> | |
| 17 <data format="txt" name="outputs" label="All Outputs"/> | |
| 18 <data format="txt" name="logs" label="All Logs"/> | |
| 19 </outputs> | |
| 20 <help> | |
| 21 | |
| 22 | |
| 23 .. class:: infomark | |
| 24 | |
| 25 **Program encapsulated in Galaxy by Southgreen** | |
| 26 | |
| 27 .. class:: infomark | |
| 28 | |
| 29 **Admixture version 1.23** | |
| 30 | |
| 31 ----- | |
| 32 | |
| 33 ============== | |
| 34 Please cite: | |
| 35 ============== | |
| 36 | |
| 37 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 =========== | |
| 42 Overview: | |
| 43 =========== | |
| 44 | |
| 45 ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). | |
| 46 | |
| 47 ----- | |
| 48 | |
| 49 For further informations, please visite the Admixture_ website. | |
| 50 | |
| 51 | |
| 52 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html | |
| 53 </help> | |
| 54 | |
| 55 </tool> |