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1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1">
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2 <description>checks concordance between input files for GWAS analysis</description>
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4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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5 <requirements>
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6 <requirement type="binary">perl</requirement>
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7 </requirements>
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8
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9 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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10 <stdio>
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11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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14
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15 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
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16 </command>
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17 <inputs>
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18 <param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
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19 <param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
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20 </inputs>
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21 <outputs>
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22 <data format="txt" name="out_hapmap" label="Hapmap output"/>
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23 <data format="txt" name="out_trait" label="Trait output"/>
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24 <data format="txt" name="stats" label="Logfile and statistics"/>
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25 </outputs>
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26
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27 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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28 <tests>
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29 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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30 <!-- [HELP] Multiple tests can be defined with different parameters -->
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31 <test>
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32 <param name="hapmap" value="gwas-hapmap" />
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33 <param name="trait" value="gwas-trait" />
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34 <output name="out_hapmap" file="gwas-result.hapmap" />
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35 <output name="out_trait" file="gwas-result.trait" />
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36 <output name="stats" file="gwas-result.stats" />
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37 </test>
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38 </tests>
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39 <help>
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40
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41 <![CDATA[
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42
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43
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44 .. class:: infomark
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45
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46 **Authors** South Green
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47
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48 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
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49
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50 .. class:: infomark
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51
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52 **Galaxy integration** South Green.
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53
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54 ---------------------------------------------------
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55
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56
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57 ===============
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58 CheckGWASInputs
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59 ===============
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60
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61 -----------
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62 Description
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63 -----------
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64
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65 | CheckGWASInputs checks concordance between input files for GWAS analysis.
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66
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67
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68 -----------------
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69 Workflow position
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70 -----------------
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71
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72 **Upstream tool**
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73
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74 =============== ====================== ===========
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75 Name output file(s) format
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76 =============== ====================== ===========
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77 VCF to Hapmap Hapmap file hapmap
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78 =============== ====================== ===========
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79
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80
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81
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82
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83 ----------
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84 Input file
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85 ----------
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86
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87 Hapmap file
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88 Allelic file in Hapmap format
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89
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90 Trait file
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91 Phenotypic file
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92
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93 ------------
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94 Output files
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95 ------------
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96
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97 Hapmap output
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98
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99 Trait output
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100
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101 Logfile and statistics
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102
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103 ---------------------------------------------------
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104
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105 ---------------
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106 Working example
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107 ---------------
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108
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109 Input files
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110 ===========
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111
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112 Hapmap file
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113 -----------
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114
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115 ::
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116
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117 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2
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118 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA
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119 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA
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120
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121 Trait file
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122 ----------
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123
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124 ::
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125
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126 <Trait> Test
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127 Ind1 -2.9985936006411
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128 Ind2 -2.68669426456267
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129
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130 Output files
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131 ============
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132
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133 Hapmap output
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134 -------------
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135
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136 ::
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137
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138 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4
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139 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA
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140 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT
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141
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142
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143 Trait output
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144 ------------
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145
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146 ::
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147
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148 <Trait> Test
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149 Ind429 -26.2142525264157
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150 Ind373 12.0306115988504
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151 Ind81 1.98118654229534
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152
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153 Logfile and statistics
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154 ----------------------
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155
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156 ::
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157
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158
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159 ==============================================
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160 Individuals
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161 ==============================================
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162 Individuals in hapmap file: 500
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163 Individuals in trait file: 500
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164 Individuals found in both files: 500
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165 ==============================================
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166 Markers
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167 ==============================================
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168 Discarded markers:
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169 Monomorphic: 0
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170 Not biallelic: 0
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171 Modified markers:
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172 Difference in variation: 0
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173
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174 ]]>
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175
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176
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177 </help>
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178 <citations>
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179 <!-- [HELP] As DOI or BibTex entry -->
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180 <citation type="bibtex">@article{Dereeper03062015,
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181 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
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182 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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183 year = {2015},
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184 doi = {10.1093/nar/gkv351},
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185 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
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186 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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187 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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188 journal = {Nucleic Acids Research}
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189 }
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190
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191 </citation>
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192
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193 </citations>
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194 </tool>
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