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1 <tool id="rgEigPCA1" name="Eigensoft:">
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2 <description>PCA Ancestry using SNP</description>
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3
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4 <command interpreter="python">
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5 rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
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6 "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
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7 </command>
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8
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9 <inputs>
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10
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11 <param name="i" type="data" label="Input genotype data file"
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12 size="120" format="ldindep" />
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13 <param name="title" type="text" value="Ancestry PCA" label="Title for outputs from this run"
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14 size="80" />
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15 <param name="k" type="integer" value="4" label="Number of principal components to output"
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16 size="3" />
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17 <param name="m" type="integer" value="0" label="Max. outlier removal iterations"
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18 help="To turn on outlier removal, set m=5 or so. Do this if you plan on adjusting any analyses"
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19 size="3" />
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20 <param name="t" type="integer" value="5" label="# principal components used for outlier removal"
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21 size="3" />
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22 <param name="s" type="integer" value="6" label="#SDs for outlier removal"
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23 help = "Any individual with SD along one of k top principal components > s will be removed as an outlier."
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24 size="3" />
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25
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26 </inputs>
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27
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28 <outputs>
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29 <data name="out_file1" format="html" label="${title}_rgEig.html"/>
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30 <data name="pca" format="txt" label="${title}_rgEig.txt"/>
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31 </outputs>
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32
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33 <tests>
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34 <test>
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35 <param name='i' value='tinywga' ftype='ldindep' >
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36 <metadata name='base_name' value='tinywga' />
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37 <composite_data value='tinywga.bim' />
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38 <composite_data value='tinywga.bed' />
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39 <composite_data value='tinywga.fam' />
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40 <edit_attributes type='name' value='tinywga' />
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41 </param>
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42 <param name='title' value='rgEigPCAtest1' />
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43 <param name="k" value="4" />
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44 <param name="m" value="2" />
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45 <param name="t" value="2" />
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46 <param name="s" value="2" />
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47 <output name='out_file1' file='rgtestouts/rgEigPCA/rgEigPCAtest1.html' ftype='html' compare='diff' lines_diff='195'>
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48 <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="3000"/>
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49 </output>
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50 <output name='pca' file='rgtestouts/rgEigPCA/rgEigPCAtest1.txt' compare='diff'/>
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51 </test>
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52 </tests>
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53
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54 <help>
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55
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56
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57 **Syntax**
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58
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59 - **Genotype data** is an input genotype dataset in Plink lped (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) format. See below for notes
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60 - **Title** is used to name the output files so you can remember what the outputs are for
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61 - **Tuning parameters** are documented in the Eigensoft (http://genepath.med.harvard.edu/~reich/Software.htm) documentation - see below
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62
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63
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64 -----
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65
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66 **Summary**
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67
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68 Eigensoft requires ld-reduced genotype data.
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69 Galaxy has an automatic converter for genotype data in Plink linkage pedigree (lped) format.
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70 For details of this generic genotype format, please see the Plink documentation at
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71 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
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72
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73 Reading that documentation, you'll see that the linkage pedigree format is really two related files with the same
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74 file base name - a map and ped file - eg 'mygeno.ped' and 'mygeno.map'.
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75 The map file has the chromosome, offset, genetic offset and snp name corresponding to each
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76 genotype stored as separate alleles in the ped file. The ped file has family id, individual id, father id (or 0), mother id
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77 (or 0), gender (1=male, 2=female, 0=unknown) and affection (1=unaffected, 2=affected, 0=unknown),
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78 then two separate allele columns for each genotype.
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79
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80 Once you have your data in the right format, you can upload those into your Galaxy history using the "upload" tool.
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81
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82 To upload your lped data in the upload tool, choose 'lped' as the 'file format'. The tool form will change to
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83 allow you to navigate to and select each member of the pair of ped and map files stored on your local computer
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84 (or available at a public URL for Galaxy to grab).
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85 Give the dataset a meaningful name (replace rgeneticsData with something more useful!) and click execute.
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86
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87 When the upload is done, your new lped format dataset will appear in your history and then,
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88 when you choose the ancestry tool, that history dataset will be available as input.
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89
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90 **Warning for the Impatient**
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91
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92 When you execute the tool, it will look like it has not started running for a while as the automatic converter
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93 reduces the amount of LD - otherwise eigenstrat gives biased results.
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94
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95
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96 **Attribution**
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97
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98 This tool runs and relies on the work of many others, including the
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99 maintainers of the Eigensoft program, and the R and
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100 Bioconductor projects. For full attribution, source code and documentation, please see
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101 http://genepath.med.harvard.edu/~reich/Software.htm, http://cran.r-project.org/
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102 and http://www.bioconductor.org/ respectively
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103
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104 This implementation is a Galaxy tool wrapper around these third party applications.
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105 It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
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106 ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
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107
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108 copyright Ross Lazarus 2007
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109 Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
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110 but is about as useful as a sponge boat without EIGENSOFT pca code.
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111
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112 **README from eigensoft2 distribution at http://genepath.med.harvard.edu/~reich/Software.htm**
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113
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114 [rerla@beast eigensoft2]$ cat README
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115 EIGENSOFT version 2.0, January 2008 (for Linux only)
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116
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117 This is the same as our EIGENSOFT 2.0 BETA release with a few recent changes
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118 as described at http://genepath.med.harvard.edu/~reich/New_In_EIGENSOFT.htm.
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119
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120 Features of EIGENSOFT version 2.0 include:
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121 -- Keeping track of ref/var alleles in all file formats: see CONVERTF/README
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122 -- Handling data sets up to 8 billion genotypes: see CONVERTF/README
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123 -- Output SNP weightings of each principal component: see POPGEN/README
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124
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125 The EIGENSOFT package implements methods from the following 2 papers:
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126 Patterson N. et al. 2006 PLoS Genetics in press (population structure)
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127 Price A.L. et al. 2006 NG 38:904-9 (EIGENSTRAT stratification correction)
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128
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129 See POPGEN/README for documentation of population structure programs.
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130
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131 See EIGENSTRAT/README for documentation of EIGENSTRAT programs.
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132
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133 See CONVERTF/README for documentation of programs for converting file formats.
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134
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135
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136 Executables and source code:
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137 ----------------------------
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138 All C executables are in the bin/ directory.
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139
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140 We have placed source code for all C executables in the src/ directory,
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141 for users who wish to modify and recompile our programs. For example, to
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142 recompile the eigenstrat program, type
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143 "cd src"
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144 "make eigenstrat"
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145 "mv eigenstrat ../bin"
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146
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147 Note that some of our software will only compile if your system has the
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148 lapack package installed. (This package is used to compute eigenvectors.)
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149 Some users may need to change "blas-3" to "blas" in the Makefile,
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150 depending on how blas and lapack are installed.
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151
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152 If cc is not available on your system, try "cp Makefile.alt Makefile"
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153 and then recompile.
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154
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155 If you have trouble compiling and running our code, try compiling and
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156 running the pcatoy program in the src directory:
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157 "cd src"
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158 "make pcatoy"
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159 "./pcatoy"
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160 If you are unable to run the pcatoy program successfully, please contact
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161 your system administrator for help, as this is a systems issue which is
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162 beyond our scope. Your system administrator will be able to troubleshoot
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163 your systems issue using this trivial program. [You can also try running
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164 the pcatoy program in the bin directory, which we have already compiled.]
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165 </help>
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166 </tool>
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167
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