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2
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1 <tool id="xseeker_preparator"
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2 name="XSeeker Preparator"
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16
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3 version="1.2.3"
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2
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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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16
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13 <requirement type="package" >bioconductor-xcms</requirement>
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14 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
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15 <requirement type="package" >git</requirement>
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16 <requirement type="package" >r-blob</requirement>
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17 <requirement type="package" >r-dbi</requirement>
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18 <requirement type="package" >r-fst</requirement>
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19 <requirement type="package" >r-optparse</requirement>
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20 <requirement type="package" >r-stringr</requirement>
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21 <requirement type="package" >r-purrr</requirement>
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22 <requirement type="package" >r-rsqlite</requirement>
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23 <requirement type="package" >r-dbmodelr</requirement>
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24 <!--
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4
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25 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
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15
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26 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
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14
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27 <requirement type="package" version="2.29.2">git</requirement>
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4
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28 <requirement type="package" version="1.2.1">r-blob</requirement>
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29 <requirement type="package" version="1.1.0">r-dbi</requirement>
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30 <requirement type="package" version="0.9.4">r-fst</requirement>
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31 <requirement type="package" version="1.6.6">r-optparse</requirement>
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32 <requirement type="package" version="1.4.0">r-stringr</requirement>
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33 <requirement type="package" version="0.3.4">r-purrr</requirement>
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34 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
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14
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35 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
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16
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36 -->
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2
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37 </requirements>
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38 <stdio>
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39
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40 <exit_code
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41 range="1"
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42 level="warning"
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43 description="Selected samples have no data associated to them."
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44 />
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45
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46 <exit_code
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47 range="2"
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48 level="warning"
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49 description="Some samples have no data associated to them."
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50 />
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51
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52 </stdio>
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53
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54 <version_command>
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4
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55 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
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2
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56 </version_command>
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57
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58 <command>
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59 <![CDATA[
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4
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60 Rscript '$__tool_directory__/XSeekerPreparator.R'
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2
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61
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62 -P
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63
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64 --input '$input'
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65 --output '$output'
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66
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67 #if $samples.selected
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4
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68 --samples '${",".join($samples.selected)}'
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2
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69 #end if
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70
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71 #if $database.archetypes
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72 --archetype '${",".join($database.archetypes)}'
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73 #end if
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74
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75 #if $database.base.kind == "tabular"
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76 --compounds-csv '${database.base.tabular}'
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77 #else if $database.base.kind == "sql"
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78 --database '${database.base.sql}'
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79 #end if
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80
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81 #if $database.models.kind == "default"
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82 --models '${base_config}'
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83 #else
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84 --models '${database.models.url}'
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85 #end if
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86
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87 ]]>
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88
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89 </command>
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90
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91 <inputs>
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92 <param
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93 name="input"
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94 type="data"
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95 multiple="false"
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96 label="Rdata to prepare"
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97 optional="false"
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98 format="rdata"
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99 >
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100 </param>
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101 <section name="samples" title="Samples Options" expanded="false">
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102 <param
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103 name="selected"
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104 type="data"
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105 multiple="true"
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106 label="Samples to visualize"
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107 optional="true"
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108 format="mzml"
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109 >
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110 </param>
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111 </section>
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112
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113 <section name="database" title="Database Options" expanded="false">
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114 <param
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115 name="archetypes"
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116 type="select"
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117 multiple="true"
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118 label="Molecule family (for database's compounds enrichment)"
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119 >
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120 <option value="G" selected="true">General</option>
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121 <option value="H">Halogenates</option>
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122 </param>
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123
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124 <conditional name="base">
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125 <param name="kind" type="select" label="File containing compound's type">
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126 <option value="none" selected="true">None (deafult)</option>
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127 <option value="tabular">tabular</option>
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128 <option value="sql">sql</option>
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129 </param>
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130 <when value="tabular">
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131 <param
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132 name="tabular"
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133 type="data"
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134 multiple="true"
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135 label="Tabular file containing compound to use in XSeeker"
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136 optional="true"
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137 format="tabular"
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138 >
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139 </param>
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140 </when>
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141 <when value="sql">
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142 <param
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143 name="sql"
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144 type="data"
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145 multiple="true"
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146 label="SQL file containing compound to use in XSeeker"
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147 optional="true"
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148 format="sql"
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149 >
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150 </param>
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151 </when>
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152 </conditional>
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153
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154 <conditional name="models">
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155 <param name="kind" type="select" label="How is the database's model defined">
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156 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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157 <option value="url">Download model file</option>
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158 <option value="git">Get versionned model file</option>
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159 </param>
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160 <when value="url">
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161 <param name="url" type="text" format="url" label="File URL"/>
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162 </when>
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163 <when value="git">
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164 <param name="url" type="text" format="url" label="Repo URL"/>
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165 </when>
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166 </conditional>
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167 </section>
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168 </inputs>
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169
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170
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171 <outputs>
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3
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172 <data format="sqlite" name="output" />
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4
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173 <!-- <data format="xseeker.sqlite" name="output" /> -->
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2
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174 </outputs>
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175
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176 <configfiles>
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177 <configfile name="base_config">
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178 tryCatch({
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179 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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180 }, error=function(e) {
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181 stop("Please, install DBModelR before you source this file.")
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182 })
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183
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184 list(
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185 adduct=DBModelR::ModelDefinition(
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186 table="adduct",
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187 fields=list(
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188 name="TEXT",
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189 mass="FLOAT",
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190 charge="INTEGER",
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191 multi="INTEGER",
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192 formula_add="TEXT",
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193 formula_ded="TEXT",
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194 sign="TEXT",
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195 oidscore="INTEGER",
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196 quasi="INTEGER",
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197 ips="FLOAT"
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198 )
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199 ),
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200 cluster=DBModelR::ModelDefinition(
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201 table="cluster",
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202 fields=list(
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203 clusterID="INTEGER",
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204 formula="TEXT",
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205 annotation="TEXT",
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206 coeff="FLOAT",
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207 r_squared="FLOAT",
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208 charge="INTEGER",
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209 mean_rt="FLOAT",
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210 score="FLOAT",
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211 deviation="FLOAT",
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212 status="TEXT",
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213 curent_group="INTEGER",
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214 pc_group="INTEGER",
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215 align_group="INTEGER",
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216 xcms_group="INTEGER"
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217 ),
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12
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218 one=list("sample", "compound", "adduct")
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2
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219 ),
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220 compound=DBModelR::ModelDefinition(
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221 table="compound",
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222 fields=list(
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223 name="TEXT",
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224 common_name="TEXT",
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225 formula="TEXT",
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226 charge="INTEGER",
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227 date="TEXT",
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228 mz="FLOAT"
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229 )
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230 ),
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231 feature=DBModelR::ModelDefinition(
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232 table="feature",
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233 fields=list(
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234 featureID="INTEGER",
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235 mz="FLOAT",
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236 mz_min="FLOAT",
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237 mz_max="FLOAT",
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238 rt="FLOAT",
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239 rt_min="FLOAT",
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240 rt_max="FLOAT",
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241 int_o="FLOAT",
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242 int_b="FLOAT",
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243 max_o="FLOAT",
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244 iso="TEXT",
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245 abundance="FLOAT"
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246 ),
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247 one=list("cluster")
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248 ),
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249 instrument=DBModelR::ModelDefinition(
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250 table="instrument",
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251 fields=list(
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252 model="TEXT",
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253 manufacturer="TEXT",
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254 analyzer="TEXT",
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255 detector_type="TEXT",
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256 ion_source="TEXT"
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257 )
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258 ),
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259 instrument_config=DBModelR::ModelDefinition(
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260 table="instrument_config",
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261 fields=list(
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262 resolution="TEXT",
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263 agc_target="TEXT",
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264 maximum_IT="TEXT",
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265 number_of_scan_range="TEXT",
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266 scan_range="TEXT",
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267 version="TEXT"
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268 )
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269 ),
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270 project=DBModelR::ModelDefinition(
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271 table="project",
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272 fields=list(
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273 name="TEXT",
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274 comment="TEXT"
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275 ),
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276 one=list("sample")
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277 ),
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278 sample=DBModelR::ModelDefinition(
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279 table="sample",
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280 fields=list(
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281 name="TEXT",
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282 path="TEXT",
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283 polarity="TEXT",
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284 kind="TEXT", ## rdata or mxml or enriched_rdata
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285 raw="BLOB"
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286 ),
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287 one=list(
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288 "peak_picking_parameters",
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289 "pairing_parameters",
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290 "alignmenmt_parameters",
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291 "camera_parameters",
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292 "instrument",
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293 "instrument_config",
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294 "software",
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295 "smol_xcms_set"
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296 )
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297 ),
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298 smol_xcms_set=DBModelR::ModelDefinition(
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299 table="smol_xcms_set",
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300 fields=list(
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301 raw="BLOB"
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302 )
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303 ),
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304 software=DBModelR::ModelDefinition(
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305 table="software",
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306 fields=list(
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307 name="TEXT",
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308 version="TEXT"
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309 )
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310 ),
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311 peak_picking_parameters=DBModelR::ModelDefinition(
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312 table="peak_picking_parameters",
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313 fields=list(
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314 ppm="FLOAT",
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315 peakwidth="TEXT",
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316 snthresh="TEXT",
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317 prefilterStep="TEXT",
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318 prefilterLevel="TEXT",
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319 mzdiff="TEXT",
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320 fitgauss="TEXT",
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321 noise="TEXT",
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322 mzCenterFun="TEXT",
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323 integrate="INTEGER",
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324 firstBaselineCheck="TEXT",
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325 snthreshIsoROIs="TEXT",
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326 maxCharge="INTEGER",
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327 maxIso="INTEGER",
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328 mzIntervalExtension="TEXT"
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329 )
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330 ),
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331 alignmenmt_parameters=DBModelR::ModelDefinition(
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332 table="alignmenmt_parameters",
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333 fields=list(
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334 binSize="TEXT",
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335 centerSample="TEXT",
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336 response="TEXT",
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337 distFun="TEXT",
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338 gapInit="TEXT",
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339 gapExtend="TEXT",
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340 factorDiag="TEXT",
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341 factorGap="TEXT",
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342 localAlignment="INTEGER",
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343 initPenalty="TEXT",
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344 bw="TEXT",
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345 minFraction="TEXT",
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346 minSamples="TEXT",
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347 maxFeatures="TEXT"
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348 )
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349 )
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350 )
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351 </configfile>
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352 </configfiles>
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353 </tool>
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