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19
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1 <tool id="xseeker_preparator" name="XSeeker Preparator" version="1.3.0">
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2 <description>prepares RData file from XCMS+CAMERA for XSeeker</description>
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2
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3 <edam_operations>
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4 <edam_operation>operation_1812</edam_operation>
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5 <edam_operation>operation_0335</edam_operation>
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6 </edam_operations>
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7 <requirements>
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16
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8 <requirement type="package" >bioconductor-xcms</requirement>
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9 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
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10 <requirement type="package" >git</requirement>
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11 <requirement type="package" >r-blob</requirement>
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12 <requirement type="package" >r-dbi</requirement>
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13 <requirement type="package" >r-fst</requirement>
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14 <requirement type="package" >r-optparse</requirement>
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15 <requirement type="package" >r-stringr</requirement>
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16 <requirement type="package" >r-purrr</requirement>
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17 <requirement type="package" >r-rsqlite</requirement>
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18 <requirement type="package" >r-dbmodelr</requirement>
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19 <!--
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4
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20 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
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15
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21 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
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14
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22 <requirement type="package" version="2.29.2">git</requirement>
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4
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23 <requirement type="package" version="1.2.1">r-blob</requirement>
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24 <requirement type="package" version="1.1.0">r-dbi</requirement>
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25 <requirement type="package" version="0.9.4">r-fst</requirement>
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26 <requirement type="package" version="1.6.6">r-optparse</requirement>
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27 <requirement type="package" version="1.4.0">r-stringr</requirement>
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28 <requirement type="package" version="0.3.4">r-purrr</requirement>
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29 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
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14
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30 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
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16
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31 -->
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2
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32 </requirements>
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33 <stdio>
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34 <exit_code
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35 range="1"
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36 level="warning"
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37 description="Selected samples have no data associated to them."
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38 />
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39 <exit_code
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40 range="2"
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41 level="warning"
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42 description="Some samples have no data associated to them."
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43 />
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44 </stdio>
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45 <version_command>
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4
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46 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
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2
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47 </version_command>
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48 <command>
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49 <![CDATA[
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4
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50 Rscript '$__tool_directory__/XSeekerPreparator.R'
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2
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51 -P
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52 --input '$input'
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53 --output '$output'
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54 #if $samples.selected
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4
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55 --samples '${",".join($samples.selected)}'
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2
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56 #end if
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57 #if $database.archetypes
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58 --archetype '${",".join($database.archetypes)}'
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59 #end if
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60 #if $database.base.kind == "tabular"
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61 --compounds-csv '${database.base.tabular}'
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62 #else if $database.base.kind == "sql"
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63 --database '${database.base.sql}'
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64 #end if
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65 #if $database.models.kind == "default"
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66 --models '${base_config}'
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67 #else
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68 --models '${database.models.url}'
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69 #end if
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19
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70 #if $class_column
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71 --class '${class_column}'
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72 #end if
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2
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73 ]]>
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74 </command>
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75 <inputs>
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76 <param
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77 name="input"
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78 type="data"
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79 multiple="false"
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80 label="Rdata to prepare"
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81 optional="false"
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82 format="rdata"
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83 >
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84 </param>
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19
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85 <param
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86 name="class_column"
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87 type="text"
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88 value=""
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89 label="Column class name"
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90 help="
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91 The name of the column containing the classes -
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92 leave empty to let xsprep guess
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93 "
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94 optional="true"
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95 >
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96 </param>
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2
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97 <section name="samples" title="Samples Options" expanded="false">
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98 <param
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99 name="selected"
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100 type="data"
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101 multiple="true"
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102 label="Samples to visualize"
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103 optional="true"
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104 format="mzml"
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105 >
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106 </param>
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107 </section>
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108 <section name="database" title="Database Options" expanded="false">
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109 <param
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110 name="archetypes"
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111 type="select"
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112 multiple="true"
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113 label="Molecule family (for database's compounds enrichment)"
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114 >
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115 <option value="G" selected="true">General</option>
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116 <option value="H">Halogenates</option>
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117 </param>
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118 <conditional name="base">
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119 <param name="kind" type="select" label="File containing compound's type">
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120 <option value="none" selected="true">None (deafult)</option>
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121 <option value="tabular">tabular</option>
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122 <option value="sql">sql</option>
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123 </param>
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124 <when value="tabular">
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125 <param
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126 name="tabular"
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127 type="data"
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128 multiple="true"
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129 label="Tabular file containing compound to use in XSeeker"
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130 optional="true"
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131 format="tabular"
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132 >
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133 </param>
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134 </when>
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135 <when value="sql">
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136 <param
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137 name="sql"
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138 type="data"
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139 multiple="true"
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140 label="SQL file containing compound to use in XSeeker"
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141 optional="true"
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142 format="sql"
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143 >
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144 </param>
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145 </when>
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146 </conditional>
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147 <conditional name="models">
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148 <param name="kind" type="select" label="How is the database's model defined">
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149 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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150 <option value="url">Download model file</option>
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151 <option value="git">Get versionned model file</option>
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152 </param>
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153 <when value="url">
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154 <param name="url" type="text" format="url" label="File URL"/>
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155 </when>
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156 <when value="git">
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157 <param name="url" type="text" format="url" label="Repo URL"/>
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158 </when>
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159 </conditional>
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160 </section>
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161 </inputs>
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162 <outputs>
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3
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163 <data format="sqlite" name="output" />
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4
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164 <!-- <data format="xseeker.sqlite" name="output" /> -->
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2
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165 </outputs>
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166 <configfiles>
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167 <configfile name="base_config">
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168 tryCatch({
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169 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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170 }, error=function(e) {
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171 stop("Please, install DBModelR before you source this file.")
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172 })
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173 list(
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19
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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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2
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187 )
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188 ),
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19
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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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2
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207 ),
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19
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208 one = list("compound", "adduct"),
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209 many = list("sample")
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2
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210 ),
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19
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211 compound = DBModelR::ModelDefinition(
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212 table = "compound",
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213 fields = list(
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214 name = "TEXT",
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215 common_name = "TEXT",
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216 formula = "TEXT",
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217 charge = "INTEGER",
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218 date = "TEXT",
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219 mz = "FLOAT"
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2
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220 )
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221 ),
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19
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222 feature = DBModelR::ModelDefinition(
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223 table = "feature",
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224 fields = list(
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225 featureID = "INTEGER",
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226 mz = "FLOAT",
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227 mz_min = "FLOAT",
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228 mz_max = "FLOAT",
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229 rt = "FLOAT",
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230 rt_min = "FLOAT",
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231 rt_max = "FLOAT",
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232 int_o = "FLOAT",
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233 int_b = "FLOAT",
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234 max_o = "FLOAT",
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235 iso = "TEXT",
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236 abundance = "FLOAT"
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2
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237 ),
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19
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238 one = list("cluster"),
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239 many = list("sample")
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2
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240 ),
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19
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241 instrument = DBModelR::ModelDefinition(
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242 table = "instrument",
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243 fields = list(
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244 model = "TEXT",
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245 manufacturer = "TEXT",
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246 analyzer = "TEXT",
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247 detector_type = "TEXT",
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248 ion_source = "TEXT"
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2
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249 )
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250 ),
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19
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251 instrument_config = DBModelR::ModelDefinition(
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252 table = "instrument_config",
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253 fields = list(
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254 resolution = "TEXT",
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255 agc_target = "TEXT",
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256 maximum_IT = "TEXT",
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257 number_of_scan_range = "TEXT",
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258 scan_range = "TEXT",
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259 version = "TEXT"
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2
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260 )
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261 ),
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19
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262 project = DBModelR::ModelDefinition(
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263 table = "project",
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264 fields = list(
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265 name = "TEXT",
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266 comment = "TEXT"
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2
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267 ),
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19
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268 one = list("sample")
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2
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269 ),
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19
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270 sample = DBModelR::ModelDefinition(
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271 table = "sample",
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272 fields = list(
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273 name = "TEXT",
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274 path = "TEXT",
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275 polarity = "TEXT",
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276 kind = "TEXT", ## rdata or mxml or enriched_rdata
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277 raw = "BLOB"
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2
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278 ),
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19
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279 one = list(
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2
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280 "peak_picking_parameters",
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281 "pairing_parameters",
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282 "alignmenmt_parameters",
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283 "camera_parameters",
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284 "instrument",
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285 "instrument_config",
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286 "software",
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287 "smol_xcms_set"
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288 )
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289 ),
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19
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290 smol_xcms_set = DBModelR::ModelDefinition(
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291 table = "smol_xcms_set",
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292 fields = list(
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293 raw = "BLOB"
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2
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294 )
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295 ),
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19
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296 software = DBModelR::ModelDefinition(
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297 table = "software",
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298 fields = list(
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299 name = "TEXT",
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300 version = "TEXT"
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2
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301 )
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302 ),
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19
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303 peak_picking_parameters = DBModelR::ModelDefinition(
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304 table = "peak_picking_parameters",
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305 fields = list(
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306 ppm = "FLOAT",
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307 peakwidth = "TEXT",
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308 snthresh = "TEXT",
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309 prefilterStep = "TEXT",
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310 prefilterLevel = "TEXT",
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311 mzdiff = "TEXT",
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312 fitgauss = "TEXT",
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313 noise = "TEXT",
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314 mzCenterFun = "TEXT",
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315 integrate = "INTEGER",
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316 firstBaselineCheck = "TEXT",
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317 snthreshIsoROIs = "TEXT",
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318 maxCharge = "INTEGER",
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319 maxIso = "INTEGER",
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320 mzIntervalExtension = "TEXT"
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2
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321 )
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322 ),
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19
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323 alignmenmt_parameters = DBModelR::ModelDefinition(
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324 table = "alignmenmt_parameters",
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325 fields = list(
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326 binSize = "TEXT",
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327 centerSample = "TEXT",
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328 response = "TEXT",
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329 distFun = "TEXT",
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330 gapInit = "TEXT",
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331 gapExtend = "TEXT",
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332 factorDiag = "TEXT",
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333 factorGap = "TEXT",
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334 localAlignment = "INTEGER",
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335 initPenalty = "TEXT",
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336 bw = "TEXT",
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337 minFraction = "TEXT",
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338 minSamples = "TEXT",
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339 maxFeatures = "TEXT"
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2
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340 )
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341 )
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342 )
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343 </configfile>
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344 </configfiles>
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345 </tool>
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