Mercurial > repos > iuc > gemini_load

annotate gemini_load.xml @ 8:45296e47d565 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author iuc
date Tue, 10 Mar 2020 06:16:34 -0400
parents 64132aa2d62a
children 2270a8b83c12
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
0
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2 <description>Loading a VCF file into GEMINI</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">load</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
4
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12 @PROVIDE_ANNO_DATA@
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14 ## gemini load expects a bgzipped and tabixed vcf as input
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15 #set $tabixed_file = 'input.vcf.gz'
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16 #if $infile.ext == 'vcf':
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17 bgzip -c '$infile' > $tabixed_file &&
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18 tabix -p vcf $tabixed_file &&
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19 #else:
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20 ln -s '$infile' $tabixed_file &&
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21 ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi &&
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22 #end if
0
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24 gemini
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25 @BINARY@
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26 -v input.vcf.gz
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27 #if str( $annotation_type ) != "None":
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28 -t $annotation_type
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29 #end if
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30
5
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31 $has_genotypes
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32
0
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33 #if $ped:
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34 -p $ped
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35 #end if
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36
5
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37 #if 'gerp_bp' not in str($opt_content):
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38 --skip-gerp-bp
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39 #end if
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40 #if 'cadd' not in str($opt_content):
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41 --skip-cadd
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42 #end if
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43 #if 'gene_tables' not in str($opt_content):
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44 --skip-gene-tables
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45 #end if
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46 #if 'genotypes' not in str($opt_content):
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47 --no-load-genotypes
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48 #end if
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49 #if 'gt_pl' not in str($opt_content):
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50 --skip-pls
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51 #end if
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52 #if 'passonly' in str($opt_content):
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53 --passonly
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54 #end if
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55 #if 'info_string' in str($opt_content):
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56 --save-info-string
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57 #end if
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58
0
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59 --cores \${GALAXY_SLOTS:-4}
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60
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61 '$outfile'
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62 ]]>
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63 </command>
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64 <inputs>
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65 <param name="infile" type="data" format="vcf,vcf_bgzip"
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66 label="VCF dataset to be loaded in the GEMINI database"
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67 help="Only build 37 (aka hg19) of the human genome is supported.">
0
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68 <options>
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69 <filter type="add_value" value="hg19" />
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70 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
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71 <filter type="add_value" value="hg_g1k_v37" />
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72 </options>
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73 </param>
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74 <param argument="-t" name="annotation_type" type="select"
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75 label="The variants in this input are"
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76 help="GEMINI can parse and use annotations generated with either snpEff (both 'EFF'- and 'ANN'-style annotations are supported) or VEP. You can also load unannotated variants, but most of GEMINI's functionality will not be available or not be very useful without annotations.">
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77 <option value="snpEff" selected="True">annotated with snpEff</option>
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78 <option value="VEP">annotated with VEP</option>
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79 <option value="None">not annotated (not recommended)</option>
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80 </param>
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81 <param argument="--no-genotypes" name="has_genotypes" type="boolean" falsevalue="--no-genotypes" truevalue="" checked="True"
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82 label="This input comes with genotype calls for its samples"
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83 help="This is usually the case, but some published datasets, like some 1000G VCFs, are missing genotype information."/>
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84 <expand macro="annotation_dir" />
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85 <param argument="-p" name="ped" type="data" format="tabular" optional="True"
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86 label="Sample and family information in PED format"
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87 help="The pedigree dataset is optional, but several GEMINI tools require the relationship between samples (i.e., the family structure) and/or the sample phenotype to be defined. The PED format is a simple tabular format (see the tool help below for details). If you choose to not provide sample information now, but later find that you need it for your analysis, you can also add it to an existing GEMINI database by using the GEMINI amend tool." />
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88 <param name="opt_content" type="select" display="checkboxes" multiple="true" optional="true"
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89 label="Load the following optional content into the database"
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90 help="The preselected defaults should be ok for most use cases (feel free to enable CADD scores for non-commercial use). If you are not interested in certain annotations, you can speed up database creation and decrease the resulting database size slightly by not loading them into the database. Note: GERP and CADD scores are optional parts of the annotation source and can only be loaded if available.">
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91 <option value="gerp_bp" selected="true">GERP scores</option>
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92 <option value="cadd" selected="false">CADD scores (non-commercial use only; see licensing note below)</option>
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93 <option value="gene_tables" selected="true">Gene tables</option>
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94 <option value="genotypes" selected="true">Sample genotypes</option>
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95 <option value="gt_pl" selected="true">Genotype likelihoods (sample PLs)</option>
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96 <option value="passonly" selected="false">only variants that passed all filters</option>
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97 <option value="info_string" selected="false">variant INFO field</option>
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98 </param>
0
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99 </inputs>
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100 <outputs>
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101 <data name="outfile" format="gemini.sqlite" />
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102 </outputs>
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103 <tests>
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104 <test>
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105 <param name="annotation_databases" value="1999-01-01" />
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106 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
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107 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
4
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108 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
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109 <assert_command>
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110 <has_text text="--skip-gerp-bp" />
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111 <has_text text="--skip-cadd" />
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112 <not_has_text text="--skip-gene-tables" />
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113 <not_has_text text="--skip-pls" />
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114 <not_has_text text="--no-load-genotypes" />
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115 <not_has_text text="--passonly" />
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116 <not_has_text text="--save-info-string" />
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117 <not_has_text text="--no-genotypes" />
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118 </assert_command>
4
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119 </test>
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120 <test>
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121 <param name="annotation_databases" value="1999-01-01" />
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122 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
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123 <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
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124 <param name="has_genotypes" value="True" />
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125 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
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126 <assert_stderr>
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127 <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
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128 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
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129 </assert_stderr>
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130 <assert_command>
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131 <not_has_text text="--skip-gerp-bp" />
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132 <not_has_text text="--skip-cadd" />
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133 <not_has_text text="--skip-gene-tables" />
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134 <not_has_text text="--skip-pls" />
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135 <not_has_text text="--no-load-genotypes" />
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136 <not_has_text text="--passonly" />
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137 <not_has_text text="--save-info-string" />
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138 <not_has_text text="--no-genotypes" />
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139 </assert_command>
4
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140 </test>
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141 <test>
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142 <param name="annotation_databases" value="1999-01-01" />
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143 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
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144 <param name="opt_content" value="genotypes,gt_pl" />
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145 <param name="has_genotypes" value="False" />
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146 <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
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147 <assert_command>
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148 <has_text text="--skip-gerp-bp" />
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149 <has_text text="--skip-cadd" />
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150 <has_text text="--skip-gene-tables" />
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151 <not_has_text text="--skip-pls" />
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152 <not_has_text text="--no-load-genotypes" />
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153 <not_has_text text="--passonly" />
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154 <not_has_text text="--save-info-string" />
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155 <has_text text="--no-genotypes" />
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156 </assert_command>
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157 </test>
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158 <test>
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159 <param name="annotation_databases" value="1999-01-01" />
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160 <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
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161 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
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162 <param name="has_genotypes" value="True" />
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163 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
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164 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
0
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165 </test>
7
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166 <test>
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167 <param name="annotation_databases" value="1999-01-01" />
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168 <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
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169 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
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170 <param name="has_genotypes" value="True" />
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171 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
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172 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
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173 </test>
0
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174 </tests>
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175 <help><![CDATA[
6
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176 .. class:: Warning mark
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177
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178 **CADD scores licensing**
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179
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180 CADD scores are freely available for non-commercial applications only. Make
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181 sure you `contact the developers <https://cadd.gs.washington.edu/contact>`__
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182 before using them in any commercial application.
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183
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184 -----
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185
0
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186 **What it does**
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187
5
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188 Before we can use GEMINI to explore genetic variation, we must first load the
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189 variant information stored in VCF format into the GEMINI database framework.
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190
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191 To fully leverage the power of GEMINI, you should first **annotate your VCF
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192 dataset** with the functional consequences of the variants using either *VEP*
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193 or *snpEff*.
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194
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195 .. class:: Warning mark
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196
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197 To avoid problems during annotation, but also during later variant queries with
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198 GEMINI tools, it is good practice to preprocess your VCF dataset even before
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199 annoation to split records with multiple alternate alleles, and to left-align
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200 and trim indels. The authors of GEMINI recommend the tool *vt* for this purpose,
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201 an equivalently good option is *bcftools norm*, and Galaxy wrappers exist for
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202 both tools.
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203
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204 In addition, you are encouraged to provide **family and sample phenotype
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205 information in PED format**, if you are planning to use GEMINI for any kind of
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206 variant identification based on inheritance patterns.
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207
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208 A PED file is simply a tabular text file (columns can be separated by either
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209 spaces or TABs, but not a mixture of the two within the same file) with the
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210 header::
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211
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212 #family_id name paternal_id maternal_id sex phenotype
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213
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214 and optional additional columns. The actual column names in the header are not
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215 fixed, but there have to be at least six columns that are interpreted as
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216 detailed next.
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217
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218 Subsequent lines describe one sample from the VCF input dataset each, where
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219
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220 - *family_id* is an alphanumeric identifier of a family
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221
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222 If the family, to which the sample belongs, is unknown, a placeholder of
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223 ``0``, ``-9`` or ``None`` can be used to indicate this fact.
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224
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225 - *name* is the identifier of the sample described by the line
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226
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227 - *paternal_id* is the identifier of the sample's father
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228
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229 If the sample's father is not available in the VCF, a placeholder of
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230 ``0``, ``-9`` or ``None`` can be used to indicate this fact.
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231
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232 - *maternal_id* is the identifier of the sample's mother
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233
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234 If the sample's mother is not available in the VCF, a placeholder of
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235 ``0``, ``-9`` or ``None`` can be used to indicate this fact.
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236
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237 - *sex* is a numeric code for the sample's sex
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238 (1=male, 2=female, any other number=unknown sex)
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239
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240 - *phenotype* is a numeric code for the sample's phenotypic affection status
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241 (1=unaffected, 2=affected)
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242
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243 If the sample's phenotype is unknown, a placeholder of ``0`` or ``-9`` can be
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244 used to indicate this fact.
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245
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246 - Optional additional columns can have any column name you like, and accept any
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247 per-sample value. The data from such extra columns will be added to the
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248 samples table of the GEMINI database so you can use them in queries. Extra
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249 columns can be used, *e.g.*, to describe additional phenotypes.
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250
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251 - If no extra columns are present in a PED file, then the header line is
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252 optional.
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253
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254 Here are two examples of valid PED file contents::
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255
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256 #family_id name paternal_id maternal_id sex phenotype hair_color
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257 1 M10475 -9 -9 1 1 brown
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258 1 M10478 M10475 M10500 2 2 brown
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259 1 M10500 -9 -9 2 2 black
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260 1 M128215 M10475 M10500 1 1 blue
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261
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262 This describes a family with two kids, in which mother and daughter, but not
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263 father and son are phenotypically affected. The file also stores the hair color
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264 of all family members.
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265
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266 ::
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267
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268 #family_id name paternal_id maternal_id sex phenotype
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269 0 M10475 0 0 -1 1
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270 0 M10478 0 0 -1 2
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271 0 M10500 0 0 -1 2
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272 0 M128215 0 0 -1 1
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273
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274 This describes the same samples as above, but without recording family
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275 structure, sex or additional traits. Only the sample phenotypes are provided.
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276 In this case (no extra columns), the header line could be omitted.
0
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277
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278 ]]></help>
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279 <expand macro="citations"/>
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280 </tool>