annotate MLMM.xml @ 1:380b364980f9 draft default tip

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1 <tool id="mlmm" name="MLMM (GWAS analysis)" version="2.0.0">
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2 <description>GWAS using Multi-Locus Mixed-Model (MLMM)</description>
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3 <requirements>
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4 <requirement type="binary">Rscript</requirement>
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5 <requirement type="binary">perl</requirement>
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6 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11 <command interpreter="bash">./MLMM.sh $geno $map $pheno $steps $method $output $pdf $kinship $rss $step_table $log</command>
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12 <inputs>
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13 <param format="txt" name="geno" type="data" label="Genotype matrix" help="NxM, N = individuals in line, M = Markers in columns, Genotype coded in 0,1,2"/>
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14 <param type="data" format="txt" name="map" label="SNP Information file" help="3 columns: SNP, Chrom, Pos"/>
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15 <param format="txt" name="pheno" type="data" label="Phenotype matrix" help="NxT, N = individuals in line, T = Trait in columns (Phenot1, Phenot2...)"/>
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16 <param type="text" name="steps" label="Maximum number of steps for the forward approach" value="10"/>
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17 <param name="method" type="select">
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18 <option value="extBIC">EBIC</option>
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19 <option value="mbonf" selected="True">MBonf</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="output" label="Association results"/>
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24 <data format="txt" name="kinship" label="Kinship matrix"/>
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25 <data format="pdf" name="pdf" label="PDF Graphical outputs"/>
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26 <data format="txt" name="rss" label="RSS"/>
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27 <data format="txt" name="step_table" label="Step Table"/>
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28 <data format="txt" name="log" label="Log file"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="geno" value="genot.txt"/>
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33 <param name="map" value="map.txt"/>
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34 <param name="pheno" value="phenot.txt"/>
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35 <param name="steps" value="10"/>
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36 <param name="method" value="mbonf"/>
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37 <output name="output" value="output.txt"/>
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38 <output name="kinship" value="kinship.txt"/>
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39 <output name="rss" value="rss.txt"/>
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40 <output name="step_table" value="step_table.txt"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44
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45
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46 .. class:: infomark
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47
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48 **MLMM** version 1.0
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49 | **Please cite** "An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.", **Segura V, Vilhjalmsson BJ, Platt A, Korte A, Seren U, Long Q, Nordborg M.**, Nature Genetics, 44: 825-830, 2012.
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50
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51 .. class:: infomark
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52
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53 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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54
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55 .. class:: infomark
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56
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57 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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58
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59 ---------------------------------------------------
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60
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61 ====
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62 MLMM
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63 ====
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64
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65 -----------
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66 Description
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67 -----------
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68
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69 | MLMM is an efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.
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70 | For further informations, please visite the MLMM website_.
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71
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72
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73 .. _website: https://sites.google.com/site/vincentosegura/mlmm
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74
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75 ------------
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76 Dependencies
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77 ------------
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78 MLMM
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79 mlmm 1.0, Based on a archive provide by Vincent Segura: https://sites.google.com/site/vincentosegura/mlmm
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80 Bioperl
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81 perl-bioperl_ 1.6.924, Conda version
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82
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83 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
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84
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85 ]]></help>
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86 <citations>
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87 <citation type="doi">10.1038/ng.2314</citation>
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88 </citations>
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89 </tool>