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1 <tool id="xseeker_pwepawatow"
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2 name="XSeeker Preparator"
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3 version="1.0.0"
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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">/home/lpavot/R/bin/Rscript</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 </requirements>
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19
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20 <stdio>
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21
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22 <exit_code
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23 range="1"
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24 level="warning"
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25 description="Selected samples have no data associated to them."
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26 />
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27
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28 <exit_code
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29 range="2"
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30 level="warning"
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31 description="Some samples have no data associated to them."
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32 />
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33
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34 </stdio>
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35
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36 <version_command>
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37 /home/lpavot/R/bin/Rscript '$__tool_directory__/XSeekerPreparator.R' -v
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38 </version_command>
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39
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40 <command>
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41 <![CDATA[
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42
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43 /home/lpavot/R/bin/Rscript '$__tool_directory__/XSeekerPreparator.R'
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44
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45 -P
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46
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47 --input '$input'
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48 --output '$output'
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49
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50 #if $samples.selected
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51 --samples '${",".join(samples.selected)}'
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52 #end if
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53
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54 #if $database.archetypes
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55 --archetype '${",".join($database.archetypes)}'
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56 #end if
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57
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58 #if $database.base.kind == "tabular"
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59 --compounds-csv '${database.base.tabular}'
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60 #else if $database.base.kind == "sql"
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61 --database '${database.base.sql}'
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62 #end if
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63
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64 #if $database.models.kind == "default"
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65 --models '${base_config}'
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66 #else
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67 --models '${database.models.url}'
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68 #end if
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69 ]]>
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70
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71 </command>
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72
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73 <inputs>
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74 <param
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75 name="input"
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76 type="data"
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77 multiple="false"
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78 label="Rdata to prepare"
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79 optional="false"
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80 format="rdata"
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81 >
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82 </param>
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83 <section name="samples" title="Samples Options" expanded="false">
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84 <param
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85 name="selected"
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86 type="data"
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87 multiple="true"
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88 label="Samples to visualize"
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89 optional="true"
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90 format="mzml"
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91 >
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92 </param>
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93 </section>
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94
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95 <section name="database" title="Database Options" expanded="false">
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96 <param
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97 name="archetypes"
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98 type="select"
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99 multiple="true"
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100 label="Molecule family (for database's compounds enrichment)"
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101 >
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102 <option value="G" selected="true">General</option>
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103 <option value="H">Halogenates</option>
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104 </param>
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105
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106 <conditional name="base">
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107 <param name="kind" type="select" label="File containing compound's type">
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108 <option value="none" selected="true">None (deafult)</option>
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109 <option value="tabular">tabular</option>
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110 <option value="sql">sql</option>
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111 </param>
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112 <when value="tabular">
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113 <param
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114 name="tabular"
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115 type="data"
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116 multiple="true"
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117 label="Tabular file containing compound to use in XSeeker"
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118 optional="true"
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119 format="tabular"
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120 >
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121 </param>
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122 </when>
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123 <when value="sql">
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124 <param
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125 name="sql"
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126 type="data"
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127 multiple="true"
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128 label="SQL file containing compound to use in XSeeker"
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129 optional="true"
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130 format="sql"
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131 >
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132 </param>
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133 </when>
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134 </conditional>
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135
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136 <conditional name="models">
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137 <param name="kind" type="select" label="How is the database's model defined">
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138 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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139 <option value="url">Download model file</option>
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140 <option value="git">Get versionned model file</option>
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141 </param>
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142 <when value="url">
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143 <param name="url" type="text" format="url" label="File URL"/>
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144 </when>
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145 <when value="git">
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146 <param name="url" type="text" format="url" label="Repo URL"/>
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147 </when>
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148 </conditional>
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149 </section>
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150 </inputs>
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151
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152
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153 <outputs>
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154 <data format="xseeker.sqlite" name="output" />
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155 </outputs>
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156
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157 <configfiles>
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158 <configfile name="base_config">
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159 tryCatch({
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160 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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161 }, error=function(e) {
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162 stop("Please, install DBModelR before you source this file.")
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163 })
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164
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165 list(
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166 adduct=DBModelR::ModelDefinition(
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167 table="adduct",
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168 fields=list(
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169 name="TEXT",
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170 mass="FLOAT",
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171 charge="INTEGER",
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172 multi="INTEGER",
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173 formula_add="TEXT",
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174 formula_ded="TEXT",
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175 sign="TEXT",
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176 oidscore="INTEGER",
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177 quasi="INTEGER",
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178 ips="FLOAT"
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179 )
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180 ),
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181 cluster=DBModelR::ModelDefinition(
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182 table="cluster",
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183 fields=list(
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184 clusterID="INTEGER",
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185 formula="TEXT",
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186 annotation="TEXT",
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187 coeff="FLOAT",
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188 r_squared="FLOAT",
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189 charge="INTEGER",
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190 mean_rt="FLOAT",
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191 score="FLOAT",
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192 deviation="FLOAT",
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193 status="TEXT",
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194 adduct="TEXT",
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195 curent_group="INTEGER",
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196 pc_group="INTEGER",
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197 align_group="INTEGER",
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198 xcms_group="INTEGER"
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199 ),
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200 one=list("sample", "compound")
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201 ),
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202 compound=DBModelR::ModelDefinition(
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203 table="compound",
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204 fields=list(
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205 name="TEXT",
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206 common_name="TEXT",
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207 formula="TEXT",
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208 charge="INTEGER",
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209 date="TEXT",
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210 mz="FLOAT"
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211 )
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212 ),
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213 feature=DBModelR::ModelDefinition(
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214 table="feature",
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215 fields=list(
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216 featureID="INTEGER",
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217 mz="FLOAT",
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218 mz_min="FLOAT",
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219 mz_max="FLOAT",
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220 rt="FLOAT",
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221 rt_min="FLOAT",
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222 rt_max="FLOAT",
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223 int_o="FLOAT",
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224 int_b="FLOAT",
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225 max_o="FLOAT",
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226 iso="TEXT",
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227 abundance="FLOAT"
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228 ),
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229 one=list("cluster")
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230 ),
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231 instrument=DBModelR::ModelDefinition(
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232 table="instrument",
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233 fields=list(
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234 model="TEXT",
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235 manufacturer="TEXT",
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236 analyzer="TEXT",
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237 detector_type="TEXT",
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238 ion_source="TEXT"
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239 )
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240 ),
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241 instrument_config=DBModelR::ModelDefinition(
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242 table="instrument_config",
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243 fields=list(
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244 resolution="TEXT",
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245 agc_target="TEXT",
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246 maximum_IT="TEXT",
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247 number_of_scan_range="TEXT",
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248 scan_range="TEXT",
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249 version="TEXT"
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250 )
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251 ),
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252 project=DBModelR::ModelDefinition(
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253 table="project",
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254 fields=list(
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255 name="TEXT",
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256 comment="TEXT"
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257 ),
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258 one=list("sample")
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259 ),
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260 sample=DBModelR::ModelDefinition(
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261 table="sample",
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262 fields=list(
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263 name="TEXT",
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264 path="TEXT",
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265 polarity="TEXT",
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266 kind="TEXT", ## rdata or mxml or enriched_rdata
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267 raw="BLOB"
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268 ),
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269 one=list(
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270 "peak_picking_parameters",
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271 "pairing_parameters",
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272 "alignmenmt_parameters",
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273 "camera_parameters",
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274 "instrument",
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275 "instrument_config",
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276 "software",
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277 "smol_xcms_set"
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278 )
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279 ),
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280 smol_xcms_set=DBModelR::ModelDefinition(
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281 table="smol_xcms_set",
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282 fields=list(
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283 raw="BLOB"
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284 )
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285 ),
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286 software=DBModelR::ModelDefinition(
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287 table="software",
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288 fields=list(
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289 name="TEXT",
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290 version="TEXT"
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291 )
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292 ),
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293 peak_picking_parameters=DBModelR::ModelDefinition(
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294 table="peak_picking_parameters",
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295 fields=list(
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296 ppm="FLOAT",
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297 peakwidth="TEXT",
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298 snthresh="TEXT",
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299 prefilterStep="TEXT",
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300 prefilterLevel="TEXT",
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301 mzdiff="TEXT",
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302 fitgauss="TEXT",
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303 noise="TEXT",
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304 mzCenterFun="TEXT",
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305 integrate="INTEGER",
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306 firstBaselineCheck="TEXT",
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307 snthreshIsoROIs="TEXT",
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308 maxCharge="INTEGER",
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309 maxIso="INTEGER",
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310 mzIntervalExtension="TEXT"
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311 )
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312 ),
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313 alignmenmt_parameters=DBModelR::ModelDefinition(
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314 table="alignmenmt_parameters",
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315 fields=list(
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316 binSize="TEXT",
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317 centerSample="TEXT",
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318 response="TEXT",
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319 distFun="TEXT",
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320 gapInit="TEXT",
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321 gapExtend="TEXT",
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322 factorDiag="TEXT",
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323 factorGap="TEXT",
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324 localAlignment="INTEGER",
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325 initPenalty="TEXT",
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326 bw="TEXT",
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327 minFraction="TEXT",
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328 minSamples="TEXT",
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329 maxFeatures="TEXT"
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330 )
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331 )
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332 )
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333 </configfile>
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334 </configfiles>
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335 </tool>
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