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1 <tool id="admixture" name="Admixture" version="1.23">
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2 <description>a population structure from large SNP genotype datasets</description>
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3 <requirements>
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4 <requirement type="package" version="1.23">admixture</requirement>
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5 </requirements>
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6 <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group
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7 </command>
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8 <inputs>
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9 <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/>
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10 <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/>
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11 <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/>
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12 <param type="text" name="kmin" label="K min" value="2"/>
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13 <param type="text" name="kmax" label="K max" value="5"/>
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14 <param type="text" name="threshold_group" label="Minimum admixture proportion percentage for group assignation" value="50"/>
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15 </inputs>
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16 <outputs>
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17 <data format="txt" name="best_k_output" label="Best K Output"/>
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18 <data format="txt" name="best_k_groups" label="Best K Groups"/>
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19 <data format="txt" name="best_k_logfile" label="Best K Logfile"/>
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20 <data format="txt" name="outputs" label="All Outputs"/>
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21 <data format="txt" name="logs" label="All Logs"/>
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22 </outputs>
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23
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24 <tests>
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25 <test>
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26 <param name="bed" value="input.bed" />
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27 <param name="bim" value="input.bim" />
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28 <param name="fam" value="input.fam" />
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29 <param name="kmax" value="3" />
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30 <param name="threshold_group" value="60" />
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31 <output name="best_k_output" file="output" />
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32 <output name="outputs" file="outputs.Q" />
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33 <output name="best_k_groups" file="groups" />
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34 </test>
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35
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36 </tests>
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37
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38 <help>
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39
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40
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41 .. class:: infomark
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42
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43 **Program encapsulated in Galaxy by Southgreen**
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44
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45 .. class:: infomark
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46
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47 **Admixture version 1.23**
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48
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49 -----
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50
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51 ==============
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52 Please cite:
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53 ==============
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54
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55 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.
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56
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57 -----
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58
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59 ===========
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60 Overview:
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61 ===========
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62
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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).
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64
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65 -----
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66
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67 For further informations, please visite the Admixture_ website.
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68
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69
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70 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
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71 </help>
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72 <citations>
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73 <citation type="doi" >10.1101/gr.094052.109</citation>
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74 </citations>
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75 </tool>
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