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2
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1 <tool id="xseeker_preparator"
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0
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2 name="XSeeker Preparator"
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9
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3 version="1.1.5"
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0
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4 >
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5 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
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6
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7 <edam_operations>
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8 <edam_operation>operation_1812</edam_operation>
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9 <edam_operation>operation_0335</edam_operation>
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10 </edam_operations>
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11
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12 <requirements>
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4
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13 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
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14 <requirement type="package">bioconductor-camera</requirement>
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15 <requirement type="package" version="2.29.2">git</requirement>
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16 <requirement type="package" version="1.2.1">r-blob</requirement>
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17 <requirement type="package" version="1.1.0">r-dbi</requirement>
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18 <requirement type="package" version="0.9.4">r-fst</requirement>
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19 <requirement type="package" version="1.6.6">r-optparse</requirement>
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20 <requirement type="package" version="1.4.0">r-stringr</requirement>
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21 <requirement type="package" version="0.3.4">r-purrr</requirement>
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22 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
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23 <requirement type="package" version="0.1.0">r-dbmodelr</requirement>
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0
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24 </requirements>
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25 <stdio>
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26
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27 <exit_code
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28 range="1"
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29 level="warning"
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30 description="Selected samples have no data associated to them."
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31 />
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32
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33 <exit_code
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34 range="2"
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35 level="warning"
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36 description="Some samples have no data associated to them."
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37 />
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38
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39 </stdio>
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40
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41 <version_command>
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4
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42 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
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43 </version_command>
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44
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45 <command>
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46 <![CDATA[
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4
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47 Rscript '$__tool_directory__/XSeekerPreparator.R'
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48
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49 -P
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50
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51 --input '$input'
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52 --output '$output'
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53
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54 #if $samples.selected
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55 --samples '${",".join($samples.selected)}'
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56 #end if
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57
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58 #if $database.archetypes
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59 --archetype '${",".join($database.archetypes)}'
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60 #end if
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61
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62 #if $database.base.kind == "tabular"
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63 --compounds-csv '${database.base.tabular}'
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64 #else if $database.base.kind == "sql"
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65 --database '${database.base.sql}'
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66 #end if
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67
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68 #if $database.models.kind == "default"
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69 --models '${base_config}'
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70 #else
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71 --models '${database.models.url}'
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72 #end if
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73
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74 ]]>
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75
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76 </command>
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77
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78 <inputs>
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79 <param
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80 name="input"
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81 type="data"
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82 multiple="false"
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83 label="Rdata to prepare"
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84 optional="false"
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85 format="rdata"
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86 >
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87 </param>
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88 <section name="samples" title="Samples Options" expanded="false">
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89 <param
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90 name="selected"
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91 type="data"
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92 multiple="true"
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93 label="Samples to visualize"
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94 optional="true"
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95 format="mzml"
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96 >
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97 </param>
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98 </section>
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99
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100 <section name="database" title="Database Options" expanded="false">
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101 <param
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102 name="archetypes"
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103 type="select"
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104 multiple="true"
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105 label="Molecule family (for database's compounds enrichment)"
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106 >
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107 <option value="G" selected="true">General</option>
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108 <option value="H">Halogenates</option>
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109 </param>
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110
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111 <conditional name="base">
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112 <param name="kind" type="select" label="File containing compound's type">
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113 <option value="none" selected="true">None (deafult)</option>
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114 <option value="tabular">tabular</option>
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115 <option value="sql">sql</option>
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116 </param>
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117 <when value="tabular">
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118 <param
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119 name="tabular"
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120 type="data"
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121 multiple="true"
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122 label="Tabular file containing compound to use in XSeeker"
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123 optional="true"
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124 format="tabular"
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125 >
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126 </param>
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127 </when>
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128 <when value="sql">
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129 <param
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130 name="sql"
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131 type="data"
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132 multiple="true"
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133 label="SQL file containing compound to use in XSeeker"
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134 optional="true"
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135 format="sql"
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136 >
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137 </param>
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138 </when>
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139 </conditional>
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140
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141 <conditional name="models">
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142 <param name="kind" type="select" label="How is the database's model defined">
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143 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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144 <option value="url">Download model file</option>
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145 <option value="git">Get versionned model file</option>
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146 </param>
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147 <when value="url">
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148 <param name="url" type="text" format="url" label="File URL"/>
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149 </when>
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150 <when value="git">
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151 <param name="url" type="text" format="url" label="Repo URL"/>
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152 </when>
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153 </conditional>
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154 </section>
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155 </inputs>
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156
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157
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158 <outputs>
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3
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159 <data format="sqlite" name="output" />
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4
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160 <!-- <data format="xseeker.sqlite" name="output" /> -->
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0
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161 </outputs>
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162
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163 <configfiles>
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164 <configfile name="base_config">
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165 tryCatch({
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166 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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167 }, error=function(e) {
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168 stop("Please, install DBModelR before you source this file.")
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169 })
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170
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171 list(
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172 adduct=DBModelR::ModelDefinition(
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173 table="adduct",
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174 fields=list(
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175 name="TEXT",
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176 mass="FLOAT",
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177 charge="INTEGER",
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178 multi="INTEGER",
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179 formula_add="TEXT",
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180 formula_ded="TEXT",
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181 sign="TEXT",
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182 oidscore="INTEGER",
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183 quasi="INTEGER",
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184 ips="FLOAT"
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185 )
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186 ),
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187 cluster=DBModelR::ModelDefinition(
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188 table="cluster",
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189 fields=list(
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190 clusterID="INTEGER",
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191 formula="TEXT",
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192 annotation="TEXT",
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193 coeff="FLOAT",
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194 r_squared="FLOAT",
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195 charge="INTEGER",
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196 mean_rt="FLOAT",
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197 score="FLOAT",
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198 deviation="FLOAT",
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199 status="TEXT",
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200 adduct="TEXT",
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201 curent_group="INTEGER",
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202 pc_group="INTEGER",
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203 align_group="INTEGER",
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204 xcms_group="INTEGER"
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205 ),
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206 one=list("sample", "compound")
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207 ),
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208 compound=DBModelR::ModelDefinition(
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209 table="compound",
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210 fields=list(
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211 name="TEXT",
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212 common_name="TEXT",
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213 formula="TEXT",
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214 charge="INTEGER",
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215 date="TEXT",
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216 mz="FLOAT"
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217 )
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218 ),
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219 feature=DBModelR::ModelDefinition(
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220 table="feature",
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221 fields=list(
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222 featureID="INTEGER",
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223 mz="FLOAT",
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224 mz_min="FLOAT",
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225 mz_max="FLOAT",
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226 rt="FLOAT",
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227 rt_min="FLOAT",
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228 rt_max="FLOAT",
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229 int_o="FLOAT",
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230 int_b="FLOAT",
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231 max_o="FLOAT",
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232 iso="TEXT",
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233 abundance="FLOAT"
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234 ),
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235 one=list("cluster")
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236 ),
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237 instrument=DBModelR::ModelDefinition(
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238 table="instrument",
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239 fields=list(
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240 model="TEXT",
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241 manufacturer="TEXT",
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242 analyzer="TEXT",
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243 detector_type="TEXT",
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244 ion_source="TEXT"
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245 )
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246 ),
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247 instrument_config=DBModelR::ModelDefinition(
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248 table="instrument_config",
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249 fields=list(
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250 resolution="TEXT",
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251 agc_target="TEXT",
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252 maximum_IT="TEXT",
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253 number_of_scan_range="TEXT",
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254 scan_range="TEXT",
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255 version="TEXT"
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256 )
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257 ),
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258 project=DBModelR::ModelDefinition(
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259 table="project",
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260 fields=list(
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261 name="TEXT",
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262 comment="TEXT"
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263 ),
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264 one=list("sample")
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265 ),
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266 sample=DBModelR::ModelDefinition(
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267 table="sample",
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268 fields=list(
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269 name="TEXT",
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270 path="TEXT",
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271 polarity="TEXT",
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272 kind="TEXT", ## rdata or mxml or enriched_rdata
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273 raw="BLOB"
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274 ),
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275 one=list(
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276 "peak_picking_parameters",
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277 "pairing_parameters",
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278 "alignmenmt_parameters",
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279 "camera_parameters",
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280 "instrument",
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281 "instrument_config",
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282 "software",
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283 "smol_xcms_set"
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284 )
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285 ),
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286 smol_xcms_set=DBModelR::ModelDefinition(
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287 table="smol_xcms_set",
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288 fields=list(
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289 raw="BLOB"
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290 )
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291 ),
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292 software=DBModelR::ModelDefinition(
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293 table="software",
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294 fields=list(
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295 name="TEXT",
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296 version="TEXT"
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297 )
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298 ),
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299 peak_picking_parameters=DBModelR::ModelDefinition(
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300 table="peak_picking_parameters",
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301 fields=list(
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302 ppm="FLOAT",
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303 peakwidth="TEXT",
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304 snthresh="TEXT",
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305 prefilterStep="TEXT",
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306 prefilterLevel="TEXT",
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307 mzdiff="TEXT",
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308 fitgauss="TEXT",
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309 noise="TEXT",
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310 mzCenterFun="TEXT",
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311 integrate="INTEGER",
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312 firstBaselineCheck="TEXT",
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313 snthreshIsoROIs="TEXT",
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314 maxCharge="INTEGER",
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315 maxIso="INTEGER",
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316 mzIntervalExtension="TEXT"
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317 )
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318 ),
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319 alignmenmt_parameters=DBModelR::ModelDefinition(
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320 table="alignmenmt_parameters",
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321 fields=list(
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322 binSize="TEXT",
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323 centerSample="TEXT",
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324 response="TEXT",
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325 distFun="TEXT",
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326 gapInit="TEXT",
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327 gapExtend="TEXT",
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328 factorDiag="TEXT",
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329 factorGap="TEXT",
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330 localAlignment="INTEGER",
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331 initPenalty="TEXT",
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332 bw="TEXT",
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333 minFraction="TEXT",
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334 minSamples="TEXT",
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335 maxFeatures="TEXT"
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336 )
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337 )
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338 )
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339 </configfile>
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340 </configfiles>
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341 </tool>
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