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1 <tool id="rgGLM1" name="Linear Models:" version="0.2">
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2 <description>for genotype data</description>
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3 <code file="rgGLM_code.py"/>
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4 <command interpreter="python">
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5 rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
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6 "$title" '$predvar' '$covar' '$out_file1' '$logf' '$i.metadata.base_name'
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7 '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
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8 </command>
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9
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10 <inputs>
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11 <page>
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12 <param name='title' label='Title for outputs' type='text' value='GLM' size="80" />
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13 <param name="i" type="data" format="pbed" label="Genotype file" size="80" />
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14 <param name="phef" type="data" format="pphe" label="Phenotype file" size="80"
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15 help="Dependent variable and covariates will be chosen from this file on the next page"/>
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16 <param name="logistic" type="text" value = "0" label="1=Use a logistic model (trait must be 1/2 coded like affection)"
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17 help="Please read the Plink documentation about this option" />
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18 <param name="gender" type="text" value = "0" label="1=Add a gender term to model" />
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19 <param name='inter' label='1=Build an interaction model - please read the docs carefully before using this'
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20 type='text' value='0' size="1" />
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21 <param name="cond" type="text" area='true' size='15x20' value = ""
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22 label="condition on this whitespace delimited rs (snp id) list" />
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23 <param name="mind" type="float" value = "0.1" label="Remove subjects with missing genotypes gt (eg 0.1)"
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24 help = "Set to 1 to include all subjects in the input file" />
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25 <param name="geno" type="float" value = "0.1" label="Remove markers with missing genotypes gt (eg 0.1)"
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26 help = "Set to 1 to include all markers in the input file" />
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27 <param name="maf" type="float" value = "0.01" label="Remove markers with MAF lt (eg 0.01) "
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28 help = "Set to 0 to include all markers in the input file"/>
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29 </page>
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30 <page>
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31 <param name="predvar" size="80" type="select" label="Dependent Trait"
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32 dynamic_options="get_phecols(phef=phef,selectOne=1)" display="radio" multiple="false"
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33 help="Model this characteristic in terms of subject snp genotypes - eg rare allele dosage for additive model" />
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34 <param name="covar" size="80" type="select" label="Covariates"
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35 dynamic_options="get_phecols(phef=phef,selectOne=0)" multiple="true" display="checkboxes"
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36 help="Use these phenotypes as covariates in models of snp dosage effects on the dependent trait"/>
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37 </page>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="tabular" name="out_file1" label="${title}_rgGLM.xls"/>
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42 <data format="txt" name="logf" label="${title}_rgGLMlog.txt" />
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43 <data format="gff" name="gffout" label="${title}_rgGLM.gff"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name='i' value='tinywga' ftype='pbed' >
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48 <metadata name='base_name' value='tinywga' />
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49 <composite_data value='tinywga.bim' />
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50 <composite_data value='tinywga.bed' />
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51 <composite_data value='tinywga.fam' />
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52 <edit_attributes type='name' value='tinywga' />
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53 </param>
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54 <param name='phef' value='tinywga' ftype='pphe' >
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55 <metadata name='base_name' value='tinywga' />
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56 <composite_data value='tinywga.pphe' />
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57 <edit_attributes type='name' value='tinywga' />
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58 </param>
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59 <param name='title' value='rgGLMtest1' />
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60 <param name='predvar' value='c1' />
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61 <param name='covar' value='None' />
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62 <param name='inter' value='0' />
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63 <param name='cond' value='' />
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64 <param name='gender' value='0' />
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65 <param name='mind' value='1.0' />
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66 <param name='geno' value='1.0' />
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67 <param name='maf' value='0.0' />
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68 <param name='logistic' value='0' />
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69 <output name='out_file1' file='rgGLMtest1_GLM.xls' ftype='tabular' compare="diff" />
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70 <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='36'/>
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71 <output name='gffout' file='rgGLMtest1_GLM_topTable.gff' compare="diff" ftype='gff' />
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72 </test>
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73 </tests>
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74 <help>
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75
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76 .. class:: infomark
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77
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78 **Syntax**
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79
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80 Note this is a two form tool - you will choose the dependent trait and covariates
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81 on the second page based on the phenotype file you choose on the first page
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82
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83 - **Genotype file** is the input Plink format compressed genotype (pbed) file
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84 - **Phenotype file** is the input Plink phenotype (pphe) file with FAMID IID followed by phenotypes
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85 - **Dependant variable** is the term on the left of the model and is chosen from the pphe columns on the second page
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86 - **Logistic** if you are (eg) using disease status as the outcome variable (case/control) - otherwise the model is linear.
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87 - **Covariates** are covariate terms on the right of the model, also chosen on the second page
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88 - **Interactions** will add interactions - please be careful how you interpret these - see the Plink documentation.
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89 - **Gender** will add gender as a model term - described in the Plink documentation
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90 - **Condition** will condition the model on one or more specific SNP rs ids as a whitespace delimited sequence
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91 - **Format** determines how your data will be returned to your Galaxy workspace
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92
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93 -----
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94
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95 .. class:: infomark
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96
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97 **Summary**
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98
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99 This tool will test GLM models for SNP predicting a dependent phenotype
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100 variable with adjustment for specified covariates.
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101
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102 If you don't see the genotype or phenotype data set you want here, it can be imported using
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103 one of the methods available from the rg get data tool group.
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104
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105 Output format can be UCSC .bed if you want to see one column of your
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106 results as a fully fledged UCSC genome browser track. A map file containing the chromosome and offset for each marker is
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107 required for writing this kind of output.
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108 Alternatively you can use .gg for the UCSC Genome Graphs tool which has all of the advantages
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109 of the the .bed track, plus a neat, visual front end that displays a lot of useful clues.
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110 Either of these are a very useful way of quickly getting a look
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111 at your data in full genomic context.
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112
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113 Finally, if you can't live without
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114 spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab
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115 delimited
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116 one with a header. Fortunately excel is dumb enough to open these without much protest.
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117
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118 -----
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119
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120 .. class:: infomark
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121
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122 **Attribution**
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123
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124 This Galaxy tool relies on Plink (see Plinksrc_) to test GLM models.
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125
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126 So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see
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127 DOC_
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128
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129 Tool and Galaxy datatypes originally designed and written for the Rgenetics
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130 series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
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131
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132 Copyright Ross Lazarus March 2007
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133 This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL.
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134
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135 I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
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136
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137 .. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/
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138
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139 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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140
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141 .. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#glm
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142
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143 </help>
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144 </tool>
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145
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146
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