Mercurial > repos > dereeper > admixture
comparison admixture.xml @ 5:97c9c8daa3c3 draft
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| author | dereeper |
|---|---|
| date | Wed, 13 Apr 2016 07:51:13 -0400 |
| parents | 58df6910f1c3 |
| children |
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| 4:58df6910f1c3 | 5:97c9c8daa3c3 |
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| 1 <tool id="admixture" name="Admixture" version="1.23"> | 1 <tool id="admixture" name="Admixture" version="1.23"> |
| 2 <description>a population structure from large SNP genotype datasets</description> | 2 <description>a population structure from large SNP genotype datasets</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.23">admixture</requirement> | 4 <requirement type="package" version="1.23">admixture</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax | 6 <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group |
| 7 </command> | 7 </command> |
| 8 <inputs> | 8 <inputs> |
| 9 <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/> | 9 <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/> |
| 10 <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/> | 10 <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/> |
| 11 <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/> | 11 <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/> |
| 12 <param type="text" name="kmin" label="K min" value="2"/> | 12 <param type="text" name="kmin" label="K min" value="2"/> |
| 13 <param type="text" name="kmax" label="K max" value="5"/> | 13 <param type="text" name="kmax" label="K max" value="5"/> |
| 14 <param type="text" name="threshold_group" label="Minimum admixture proportion percentage for group assignation" value="50"/> | |
| 14 </inputs> | 15 </inputs> |
| 15 <outputs> | 16 <outputs> |
| 16 <data format="txt" name="best_k_output" label="Best K Output"/> | 17 <data format="txt" name="best_k_output" label="Best K Output"/> |
| 18 <data format="txt" name="best_k_groups" label="Best K Groups"/> | |
| 17 <data format="txt" name="best_k_logfile" label="Best K Logfile"/> | 19 <data format="txt" name="best_k_logfile" label="Best K Logfile"/> |
| 18 <data format="txt" name="outputs" label="All Outputs"/> | 20 <data format="txt" name="outputs" label="All Outputs"/> |
| 19 <data format="txt" name="logs" label="All Logs"/> | 21 <data format="txt" name="logs" label="All Logs"/> |
| 20 </outputs> | 22 </outputs> |
| 21 | 23 |
| 23 <test> | 25 <test> |
| 24 <param name="bed" value="input.bed" /> | 26 <param name="bed" value="input.bed" /> |
| 25 <param name="bim" value="input.bim" /> | 27 <param name="bim" value="input.bim" /> |
| 26 <param name="fam" value="input.fam" /> | 28 <param name="fam" value="input.fam" /> |
| 27 <param name="kmax" value="3" /> | 29 <param name="kmax" value="3" /> |
| 28 | 30 <param name="threshold_group" value="60" /> |
| 29 <output name="best_k_output" file="output" /> | 31 <output name="best_k_output" file="output" /> |
| 30 <output name="outputs" file="outputs.Q" /> | 32 <output name="outputs" file="outputs.Q" /> |
| 33 <output name="best_k_groups" file="groups" /> | |
| 31 </test> | 34 </test> |
| 32 | 35 |
| 33 </tests> | 36 </tests> |
| 34 | 37 |
| 35 <help> | 38 <help> |
| 51 | 54 |
| 52 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. | 55 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. |
| 53 | 56 |
| 54 ----- | 57 ----- |
| 55 | 58 |
| 56 | |
| 57 =========== | 59 =========== |
| 58 Overview: | 60 Overview: |
| 59 =========== | 61 =========== |
| 60 | 62 |
| 61 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). | 63 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). |
| 65 For further informations, please visite the Admixture_ website. | 67 For further informations, please visite the Admixture_ website. |
| 66 | 68 |
| 67 | 69 |
| 68 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html | 70 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html |
| 69 </help> | 71 </help> |
| 70 | |
| 71 <citations> | 72 <citations> |
| 72 <citation type="doi" >10.1101/gr.094052.109</citation> | 73 <citation type="doi" >10.1101/gr.094052.109</citation> |
| 73 </citations> | 74 </citations> |
| 74 | |
| 75 | |
| 76 | |
| 77 </tool> | 75 </tool> |