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1 <tool id="xseeker_preparator"
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2 name="XSeeker Preparator"
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3 version="1.0.1"
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4 profile="20.04"
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5 >
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6 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
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7
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8 <edam_operations>
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9 <edam_operation>operation_1812</edam_operation>
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10 <edam_operation>operation_0335</edam_operation>
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11 </edam_operations>
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12
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13 <requirements>
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14 <requirement type="set_environment">R_SCRIPT_PATH</requirement>
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15 <!--
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16 <requirement type="package" version="4.0.0">R</requirement>
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17 -->
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18 <requirement type="package" version="4.0.0">R</requirement>
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19 <requirement type="package" version="1.6.6">optparse</requirement>
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20 <requirement type="package" version="3.10.2">xcms</requirement>
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21 <requirement type="package" version="1.2.1">blob</requirement>
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22 <requirement type="package" version="0.9.4">fst</requirement>
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23 <requirement type="package" version="1.4.0">stringr</requirement>
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24 <requirement type="package">DBModelR</requirement>
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25 </requirements>
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26
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27 <stdio>
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28
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29 <exit_code
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30 range="1"
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31 level="warning"
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32 description="Selected samples have no data associated to them."
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33 />
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34
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35 <exit_code
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36 range="2"
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37 level="warning"
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38 description="Some samples have no data associated to them."
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39 />
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40
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41 </stdio>
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42
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43 <version_command>
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44 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
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45 </version_command>
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46
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47 <command>
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48 <![CDATA[
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49
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50 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
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51
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52 -P
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53
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54 --input '$input'
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55 --output '$output'
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56
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57 #if $samples.selected
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58 --samples '${",".join(samples.selected)}'
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59 #end if
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60
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61 #if $database.archetypes
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62 --archetype '${",".join($database.archetypes)}'
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63 #end if
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64
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65 #if $database.base.kind == "tabular"
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66 --compounds-csv '${database.base.tabular}'
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67 #else if $database.base.kind == "sql"
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68 --database '${database.base.sql}'
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69 #end if
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70
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71 #if $database.models.kind == "default"
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72 --models '${base_config}'
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73 #else
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74 --models '${database.models.url}'
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75 #end if
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76
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77 ]]>
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78
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79 </command>
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80
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81 <inputs>
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82 <param
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83 name="input"
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84 type="data"
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85 multiple="false"
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86 label="Rdata to prepare"
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87 optional="false"
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88 format="rdata"
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89 >
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90 </param>
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91 <section name="samples" title="Samples Options" expanded="false">
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92 <param
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93 name="selected"
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94 type="data"
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95 multiple="true"
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96 label="Samples to visualize"
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97 optional="true"
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98 format="mzml"
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99 >
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100 </param>
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101 </section>
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102
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103 <section name="database" title="Database Options" expanded="false">
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104 <param
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105 name="archetypes"
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106 type="select"
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107 multiple="true"
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108 label="Molecule family (for database's compounds enrichment)"
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109 >
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110 <option value="G" selected="true">General</option>
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111 <option value="H">Halogenates</option>
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112 </param>
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113
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114 <conditional name="base">
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115 <param name="kind" type="select" label="File containing compound's type">
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116 <option value="none" selected="true">None (deafult)</option>
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117 <option value="tabular">tabular</option>
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118 <option value="sql">sql</option>
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119 </param>
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120 <when value="tabular">
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121 <param
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122 name="tabular"
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123 type="data"
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124 multiple="true"
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125 label="Tabular file containing compound to use in XSeeker"
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126 optional="true"
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127 format="tabular"
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128 >
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129 </param>
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130 </when>
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131 <when value="sql">
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132 <param
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133 name="sql"
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134 type="data"
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135 multiple="true"
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136 label="SQL file containing compound to use in XSeeker"
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137 optional="true"
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138 format="sql"
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139 >
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140 </param>
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141 </when>
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142 </conditional>
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143
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144 <conditional name="models">
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145 <param name="kind" type="select" label="How is the database's model defined">
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146 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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147 <option value="url">Download model file</option>
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148 <option value="git">Get versionned model file</option>
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149 </param>
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150 <when value="url">
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151 <param name="url" type="text" format="url" label="File URL"/>
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152 </when>
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153 <when value="git">
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154 <param name="url" type="text" format="url" label="Repo URL"/>
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155 </when>
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156 </conditional>
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157 </section>
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158 </inputs>
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159
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160
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161 <outputs>
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162 <data format="xseeker.sqlite" name="output" />
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163 </outputs>
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164
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165 <configfiles>
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166 <configfile name="base_config">
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167 tryCatch({
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168 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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169 }, error=function(e) {
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170 stop("Please, install DBModelR before you source this file.")
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171 })
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172
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173 list(
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174 adduct=DBModelR::ModelDefinition(
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175 table="adduct",
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176 fields=list(
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177 name="TEXT",
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178 mass="FLOAT",
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179 charge="INTEGER",
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180 multi="INTEGER",
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181 formula_add="TEXT",
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182 formula_ded="TEXT",
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183 sign="TEXT",
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184 oidscore="INTEGER",
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185 quasi="INTEGER",
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186 ips="FLOAT"
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187 )
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188 ),
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189 cluster=DBModelR::ModelDefinition(
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190 table="cluster",
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191 fields=list(
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192 clusterID="INTEGER",
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193 formula="TEXT",
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194 annotation="TEXT",
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195 coeff="FLOAT",
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196 r_squared="FLOAT",
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197 charge="INTEGER",
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198 mean_rt="FLOAT",
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199 score="FLOAT",
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200 deviation="FLOAT",
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201 status="TEXT",
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202 adduct="TEXT",
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203 curent_group="INTEGER",
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204 pc_group="INTEGER",
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205 align_group="INTEGER",
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206 xcms_group="INTEGER"
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207 ),
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208 one=list("sample", "compound")
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209 ),
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210 compound=DBModelR::ModelDefinition(
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211 table="compound",
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212 fields=list(
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213 name="TEXT",
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214 common_name="TEXT",
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215 formula="TEXT",
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216 charge="INTEGER",
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217 date="TEXT",
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218 mz="FLOAT"
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219 )
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220 ),
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221 feature=DBModelR::ModelDefinition(
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222 table="feature",
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223 fields=list(
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224 featureID="INTEGER",
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225 mz="FLOAT",
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226 mz_min="FLOAT",
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227 mz_max="FLOAT",
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228 rt="FLOAT",
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229 rt_min="FLOAT",
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230 rt_max="FLOAT",
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231 int_o="FLOAT",
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232 int_b="FLOAT",
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233 max_o="FLOAT",
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234 iso="TEXT",
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235 abundance="FLOAT"
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236 ),
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237 one=list("cluster")
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238 ),
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239 instrument=DBModelR::ModelDefinition(
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240 table="instrument",
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241 fields=list(
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242 model="TEXT",
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243 manufacturer="TEXT",
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244 analyzer="TEXT",
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245 detector_type="TEXT",
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246 ion_source="TEXT"
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247 )
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248 ),
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249 instrument_config=DBModelR::ModelDefinition(
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250 table="instrument_config",
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251 fields=list(
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252 resolution="TEXT",
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253 agc_target="TEXT",
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254 maximum_IT="TEXT",
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255 number_of_scan_range="TEXT",
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256 scan_range="TEXT",
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257 version="TEXT"
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258 )
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259 ),
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260 project=DBModelR::ModelDefinition(
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261 table="project",
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262 fields=list(
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263 name="TEXT",
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264 comment="TEXT"
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265 ),
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266 one=list("sample")
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267 ),
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268 sample=DBModelR::ModelDefinition(
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269 table="sample",
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270 fields=list(
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271 name="TEXT",
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272 path="TEXT",
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273 polarity="TEXT",
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274 kind="TEXT", ## rdata or mxml or enriched_rdata
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275 raw="BLOB"
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276 ),
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277 one=list(
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278 "peak_picking_parameters",
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279 "pairing_parameters",
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280 "alignmenmt_parameters",
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281 "camera_parameters",
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282 "instrument",
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283 "instrument_config",
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284 "software",
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285 "smol_xcms_set"
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286 )
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287 ),
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288 smol_xcms_set=DBModelR::ModelDefinition(
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289 table="smol_xcms_set",
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290 fields=list(
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291 raw="BLOB"
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292 )
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293 ),
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294 software=DBModelR::ModelDefinition(
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295 table="software",
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296 fields=list(
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297 name="TEXT",
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298 version="TEXT"
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299 )
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300 ),
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301 peak_picking_parameters=DBModelR::ModelDefinition(
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302 table="peak_picking_parameters",
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303 fields=list(
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304 ppm="FLOAT",
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305 peakwidth="TEXT",
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306 snthresh="TEXT",
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307 prefilterStep="TEXT",
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308 prefilterLevel="TEXT",
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309 mzdiff="TEXT",
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310 fitgauss="TEXT",
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311 noise="TEXT",
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312 mzCenterFun="TEXT",
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313 integrate="INTEGER",
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314 firstBaselineCheck="TEXT",
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315 snthreshIsoROIs="TEXT",
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316 maxCharge="INTEGER",
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317 maxIso="INTEGER",
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318 mzIntervalExtension="TEXT"
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319 )
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320 ),
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321 alignmenmt_parameters=DBModelR::ModelDefinition(
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322 table="alignmenmt_parameters",
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323 fields=list(
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324 binSize="TEXT",
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325 centerSample="TEXT",
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326 response="TEXT",
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327 distFun="TEXT",
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328 gapInit="TEXT",
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329 gapExtend="TEXT",
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330 factorDiag="TEXT",
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331 factorGap="TEXT",
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332 localAlignment="INTEGER",
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333 initPenalty="TEXT",
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334 bw="TEXT",
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335 minFraction="TEXT",
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336 minSamples="TEXT",
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337 maxFeatures="TEXT"
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338 )
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339 )
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340 )
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341 </configfile>
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342 </configfiles>
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343 </tool>
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