annotate XSeekerPreparator.xml @ 3:fa97d16330be draft

" master branch Updating"
author lain
date Thu, 17 Dec 2020 10:13:58 +0000
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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 >
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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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13 <requirement type="set_environment">R_SCRIPT</requirement>
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14 <requirement type="package" version="4.0.0">R</requirement>
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15 <requirement type="package" version="1.6.6">optparse</requirement>
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16 <requirement type="package" version="3.10.2">xcms</requirement>
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17 <requirement type="package" version="1.2.1">blob</requirement>
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18 <requirement type="package" version="0.9.4">fst</requirement>
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19 <requirement type="package" version="1.4.0">stringr</requirement>
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20 <requirement type="package">DBModelR</requirement>
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21 </requirements>
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22
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23 <stdio>
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24
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25 <exit_code
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26 range="1"
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27 level="warning"
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28 description="Selected samples have no data associated to them."
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29 />
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30
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31 <exit_code
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32 range="2"
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33 level="warning"
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34 description="Some samples have no data associated to them."
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35 />
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36
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37 </stdio>
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38
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39 <version_command>
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40 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
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41 </version_command>
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42
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43 <command>
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44 <![CDATA[
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45 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
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46
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47 -P
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48
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49 --input '$input'
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50 --output '$output'
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51
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52 #if $samples.selected
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53 --samples '${",".join(samples.selected)}'
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54 #end if
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55
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56 #if $database.archetypes
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57 --archetype '${",".join($database.archetypes)}'
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58 #end if
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59
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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
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66 #if $database.models.kind == "default"
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67 --models '${base_config}'
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68 #else
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69 --models '${database.models.url}'
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70 #end if
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71
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72 ]]>
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73
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74 </command>
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75
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76 <inputs>
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77 <param
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78 name="input"
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79 type="data"
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80 multiple="false"
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81 label="Rdata to prepare"
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82 optional="false"
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83 format="rdata"
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84 >
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85 </param>
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86 <section name="samples" title="Samples Options" expanded="false">
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87 <param
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88 name="selected"
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89 type="data"
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90 multiple="true"
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91 label="Samples to visualize"
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92 optional="true"
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93 format="mzml"
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94 >
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95 </param>
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96 </section>
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97
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98 <section name="database" title="Database Options" expanded="false">
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99 <param
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100 name="archetypes"
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101 type="select"
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102 multiple="true"
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103 label="Molecule family (for database's compounds enrichment)"
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104 >
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105 <option value="G" selected="true">General</option>
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106 <option value="H">Halogenates</option>
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107 </param>
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108
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109 <conditional name="base">
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110 <param name="kind" type="select" label="File containing compound's type">
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111 <option value="none" selected="true">None (deafult)</option>
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112 <option value="tabular">tabular</option>
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113 <option value="sql">sql</option>
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114 </param>
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115 <when value="tabular">
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116 <param
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117 name="tabular"
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118 type="data"
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119 multiple="true"
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120 label="Tabular file containing compound to use in XSeeker"
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121 optional="true"
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122 format="tabular"
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123 >
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124 </param>
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125 </when>
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126 <when value="sql">
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127 <param
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128 name="sql"
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129 type="data"
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130 multiple="true"
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131 label="SQL file containing compound to use in XSeeker"
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132 optional="true"
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133 format="sql"
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134 >
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135 </param>
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136 </when>
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137 </conditional>
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138
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139 <conditional name="models">
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140 <param name="kind" type="select" label="How is the database's model defined">
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141 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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142 <option value="url">Download model file</option>
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143 <option value="git">Get versionned model file</option>
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144 </param>
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145 <when value="url">
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146 <param name="url" type="text" format="url" label="File URL"/>
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147 </when>
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148 <when value="git">
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149 <param name="url" type="text" format="url" label="Repo URL"/>
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150 </when>
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151 </conditional>
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152 </section>
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153 </inputs>
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154
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155
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156 <outputs>
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157 <data format="sqlite" name="output" />
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158 </outputs>
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159
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160 <configfiles>
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161 <configfile name="base_config">
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162 tryCatch({
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163 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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164 }, error=function(e) {
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165 stop("Please, install DBModelR before you source this file.")
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166 })
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167
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168 list(
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169 adduct=DBModelR::ModelDefinition(
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170 table="adduct",
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171 fields=list(
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172 name="TEXT",
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173 mass="FLOAT",
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174 charge="INTEGER",
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175 multi="INTEGER",
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176 formula_add="TEXT",
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177 formula_ded="TEXT",
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178 sign="TEXT",
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179 oidscore="INTEGER",
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180 quasi="INTEGER",
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181 ips="FLOAT"
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182 )
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183 ),
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184 cluster=DBModelR::ModelDefinition(
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185 table="cluster",
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186 fields=list(
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187 clusterID="INTEGER",
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188 formula="TEXT",
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189 annotation="TEXT",
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190 coeff="FLOAT",
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191 r_squared="FLOAT",
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192 charge="INTEGER",
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193 mean_rt="FLOAT",
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194 score="FLOAT",
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195 deviation="FLOAT",
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196 status="TEXT",
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197 adduct="TEXT",
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198 curent_group="INTEGER",
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199 pc_group="INTEGER",
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200 align_group="INTEGER",
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201 xcms_group="INTEGER"
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202 ),
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203 one=list("sample", "compound")
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204 ),
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205 compound=DBModelR::ModelDefinition(
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206 table="compound",
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207 fields=list(
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208 name="TEXT",
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209 common_name="TEXT",
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210 formula="TEXT",
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211 charge="INTEGER",
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212 date="TEXT",
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213 mz="FLOAT"
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214 )
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215 ),
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216 feature=DBModelR::ModelDefinition(
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217 table="feature",
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218 fields=list(
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219 featureID="INTEGER",
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220 mz="FLOAT",
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221 mz_min="FLOAT",
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222 mz_max="FLOAT",
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223 rt="FLOAT",
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224 rt_min="FLOAT",
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225 rt_max="FLOAT",
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226 int_o="FLOAT",
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227 int_b="FLOAT",
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228 max_o="FLOAT",
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229 iso="TEXT",
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230 abundance="FLOAT"
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231 ),
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232 one=list("cluster")
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233 ),
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234 instrument=DBModelR::ModelDefinition(
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235 table="instrument",
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236 fields=list(
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237 model="TEXT",
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238 manufacturer="TEXT",
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239 analyzer="TEXT",
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240 detector_type="TEXT",
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241 ion_source="TEXT"
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242 )
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243 ),
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244 instrument_config=DBModelR::ModelDefinition(
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245 table="instrument_config",
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246 fields=list(
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247 resolution="TEXT",
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248 agc_target="TEXT",
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249 maximum_IT="TEXT",
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250 number_of_scan_range="TEXT",
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251 scan_range="TEXT",
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252 version="TEXT"
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253 )
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254 ),
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255 project=DBModelR::ModelDefinition(
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256 table="project",
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257 fields=list(
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258 name="TEXT",
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259 comment="TEXT"
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260 ),
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261 one=list("sample")
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262 ),
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263 sample=DBModelR::ModelDefinition(
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264 table="sample",
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265 fields=list(
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266 name="TEXT",
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267 path="TEXT",
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268 polarity="TEXT",
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269 kind="TEXT", ## rdata or mxml or enriched_rdata
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270 raw="BLOB"
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271 ),
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272 one=list(
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273 "peak_picking_parameters",
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274 "pairing_parameters",
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275 "alignmenmt_parameters",
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276 "camera_parameters",
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277 "instrument",
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278 "instrument_config",
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279 "software",
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280 "smol_xcms_set"
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281 )
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282 ),
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283 smol_xcms_set=DBModelR::ModelDefinition(
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284 table="smol_xcms_set",
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285 fields=list(
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286 raw="BLOB"
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287 )
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288 ),
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289 software=DBModelR::ModelDefinition(
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290 table="software",
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291 fields=list(
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292 name="TEXT",
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293 version="TEXT"
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294 )
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295 ),
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296 peak_picking_parameters=DBModelR::ModelDefinition(
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297 table="peak_picking_parameters",
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298 fields=list(
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299 ppm="FLOAT",
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300 peakwidth="TEXT",
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301 snthresh="TEXT",
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302 prefilterStep="TEXT",
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303 prefilterLevel="TEXT",
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304 mzdiff="TEXT",
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305 fitgauss="TEXT",
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306 noise="TEXT",
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307 mzCenterFun="TEXT",
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308 integrate="INTEGER",
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309 firstBaselineCheck="TEXT",
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310 snthreshIsoROIs="TEXT",
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311 maxCharge="INTEGER",
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312 maxIso="INTEGER",
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313 mzIntervalExtension="TEXT"
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314 )
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315 ),
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316 alignmenmt_parameters=DBModelR::ModelDefinition(
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317 table="alignmenmt_parameters",
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318 fields=list(
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319 binSize="TEXT",
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320 centerSample="TEXT",
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321 response="TEXT",
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322 distFun="TEXT",
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323 gapInit="TEXT",
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324 gapExtend="TEXT",
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325 factorDiag="TEXT",
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326 factorGap="TEXT",
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327 localAlignment="INTEGER",
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328 initPenalty="TEXT",
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329 bw="TEXT",
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330 minFraction="TEXT",
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331 minSamples="TEXT",
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332 maxFeatures="TEXT"
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333 )
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334 )
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335 )
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336 </configfile>
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337 </configfiles>
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338 </tool>