Mercurial > repos > lecorguille > camera_annotate
annotate abims_CAMERA_annotateDiffreport.xml @ 11:fc1fa0c70378 draft
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| author | lecorguille |
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| date | Mon, 04 Jul 2016 11:57:03 -0400 |
| parents | 8dd6f0ffa763 |
| children | 1c30ff90f3ae |
| rev | line source |
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1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> |
| 0 | 2 |
| 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> | |
| 4 | |
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5 <macros> |
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6 <import>macros.xml</import> |
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7 </macros> |
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8 |
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9 <expand macro="requirements"/> |
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10 <expand macro="stdio"/> |
| 0 | 11 |
| 8 | 12 <command><![CDATA[ |
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13 @COMMAND_CAMERA_SCRIPT@ |
| 8 | 14 xfunction annotatediff |
| 15 image $image | |
| 16 | |
| 17 variableMetadataOutput $variableMetadata | |
| 18 dataMatrixOutput $datamatrix | |
| 19 xsetRdataOutput $rdata | |
| 20 | |
| 21 convert_param $convert_param num_digits $num_digits | |
| 22 nSlaves \${GALAXY_SLOTS:-1} | |
| 0 | 23 sigma $sigma perfwhm $perfwhm |
| 24 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac | |
| 25 ppm $ppm mzabs $mzabs intval $intval | |
| 26 max_peaks $max_peaks | |
| 27 quick $quick_block.quick | |
| 28 #if $quick_block.quick == "FALSE" | |
| 29 polarity $quick_block.polarity | |
| 30 cor_eic_th $quick_block.cor_eic_th | |
| 31 graphMethod $quick_block.graphMethod | |
| 32 pval $quick_block.pval | |
| 33 calcCiS $quick_block.calcCiS | |
| 34 calcIso $quick_block.calcIso | |
| 35 calcCaS $quick_block.calcCaS | |
| 36 multiplier $quick_block.multiplier | |
| 37 #end if | |
| 38 | |
| 39 #if $options.option == "show": | |
| 8 | 40 runDiffreport TRUE |
| 0 | 41 eicmax $options.eicmax |
| 42 eicwidth $options.eicwidth | |
| 43 value $options.value | |
| 44 sortpval $options.sortpval | |
| 45 h $options.h | |
| 46 w $options.w | |
| 47 mzdec $options.mzdec | |
| 8 | 48 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ |
| 0 | 49 #end if |
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50 |
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51 @COMMAND_ZIPFILE_LOAD@ |
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52 |
| 8 | 53 ]]></command> |
| 0 | 54 |
| 55 <inputs> | |
| 56 | |
| 57 | |
| 58 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> | |
| 59 | |
| 60 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> | |
| 5 | 61 <param name="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" /> |
| 0 | 62 |
| 63 <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" /> | |
| 64 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" /> | |
| 65 <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" /> | |
| 66 <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" /> | |
| 67 <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" /> | |
| 68 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> | |
| 69 <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" /> | |
| 70 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> | |
| 71 <option value="into" selected="true">into</option> | |
| 72 <option value="maxo" >maxo</option> | |
| 73 <option value="intb">intb</option> | |
| 74 </param> | |
| 75 | |
| 76 | |
| 77 <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> | |
| 78 <conditional name="quick_block"> | |
| 79 <param name="quick" type="select" label="Quick mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts"> | |
| 80 <option value="TRUE">TRUE</option> | |
| 81 <option value="FALSE" selected="true">FALSE</option> | |
| 82 </param> | |
| 83 <when value="FALSE"> | |
| 84 <param name="polarity" type="select" label="findAdducts: Which polarity mode was used for measuring of the ms sample" help="polarity"> | |
| 85 <option value="positive" >positive</option> | |
| 86 <option value="negative" selected="true">negative</option> | |
| 87 </param> | |
| 88 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" /> | |
| 89 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]"> | |
| 90 <option value="hcs" selected="true">hcs</option> | |
| 91 <option value="lpc">lpc</option> | |
| 92 </param> | |
| 93 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> | |
| 94 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> | |
| 95 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> | |
| 96 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> | |
| 97 <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> | |
| 98 </when> | |
| 99 <when value="TRUE"> | |
| 100 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> | |
| 101 </when> | |
| 102 </conditional> | |
| 103 | |
| 104 | |
| 105 <!-- Annotatediffreport specific parameters --> | |
| 106 <conditional name="options"> | |
| 107 <param name="option" type="select" label="Number of condition"> | |
| 108 <option value="hide" selected="true">One condition</option> | |
| 109 <option value="show">Two or more conditions</option> | |
| 110 </param> | |
| 111 <when value="show"> | |
| 112 <param name="eicmax" type="integer" value="0" label="diffreport: number of the most significantly different analytes to create EICs for" help="[eicmax]" /> | |
| 113 <param name="eicwidth" type="integer" value="200" label="diffreport: width (in seconds) of EICs produced" help="[eicwidth]" /> | |
| 114 <param name="value" type="select" label="diffreport: Intensity values to be used for the diffreport" help="[value]"> | |
| 115 <option value="into" selected="true">into</option> | |
| 116 <option value="maxo" >maxo</option> | |
| 117 <option value="intb">intb</option> | |
| 118 </param> | |
| 119 <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> | |
| 120 <param name="w" type="integer" value="640" label="diffreport: Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> | |
| 121 <param name="mzdec" type="integer" value="2" label="diffreport: Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> | |
| 122 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> | |
| 123 </when> | |
| 124 <when value="hide"> | |
| 125 </when> | |
| 126 </conditional> | |
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127 |
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128 <expand macro="zipfile_load"/> |
| 0 | 129 </inputs> |
| 130 | |
| 131 <outputs> | |
| 3 | 132 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> |
| 0 | 133 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> |
| 134 <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > | |
| 135 <change_format> | |
| 136 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> | |
| 137 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> | |
| 138 </change_format> | |
| 3 | 139 </data> |
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140 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> |
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141 <filter>(options['option'] == 'show')</filter> |
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142 </data> |
| 0 | 143 </outputs> |
| 144 | |
| 145 <tests> | |
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146 <!--<test> |
| 0 | 147 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> |
| 148 <param name="convert_param" value="False"/> | |
| 149 <param name="num_digits" value="0"/> | |
| 150 <param name="sigma" value="6"/> | |
| 151 <param name="perfwhm" value="0.6"/> | |
| 152 <param name="maxcharge" value="3"/> | |
| 153 <param name="maxiso" value="4"/> | |
| 154 <param name="minfrac" value="0.5"/> | |
| 155 <param name="ppm" value="5"/> | |
| 156 <param name="mzabs" value="0.015"/> | |
| 157 <param name="intval" value="into"/> | |
| 158 <param name="max_peaks" value="100"/> | |
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159 <param name="quick_block|quick" value="FALSE"/> |
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160 <param name="quick_block|polarity" value="negative"/> |
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161 <param name="quick_block|cor_eic_th" value="0.75"/> |
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162 <param name="quick_block|graphMethod" value="hcs"/> |
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163 <param name="quick_block|pval" value="0.05"/> |
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164 <param name="quick_block|calcCiS" value="True"/> |
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165 <param name="quick_block|calcIso" value="False"/> |
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166 <param name="quick_block|calcCaS" value="False"/> |
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167 <param name="quick_block|multiplier" value="3"/> |
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168 <param name="options|option" value="show"/> |
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169 <param name="options|eicmax" value="200"/> |
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170 <param name="options|eicwidth" value="200"/> |
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171 <param name="options|value" value="into"/> |
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172 <param name="options|h" value="480"/> |
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173 <param name="options|w" value="640"/> |
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174 <param name="options|mzdec" value="2"/> |
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175 <param name="options|sortpval" value="False"/> |
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176 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> |
| 0 | 177 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> |
| 178 <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> | |
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179 </test>--> |
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180 <test> |
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181 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> |
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182 <param name="convert_param" value="False"/> |
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183 <param name="num_digits" value="0"/> |
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184 <param name="sigma" value="6"/> |
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185 <param name="perfwhm" value="0.6"/> |
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186 <param name="maxcharge" value="3"/> |
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187 <param name="maxiso" value="4"/> |
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188 <param name="minfrac" value="0.5"/> |
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189 <param name="ppm" value="5"/> |
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190 <param name="mzabs" value="0.015"/> |
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191 <param name="intval" value="into"/> |
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192 <param name="max_peaks" value="100"/> |
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193 <param name="quick_block|quick" value="FALSE"/> |
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194 <param name="quick_block|polarity" value="negative"/> |
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195 <param name="quick_block|cor_eic_th" value="0.75"/> |
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196 <param name="quick_block|graphMethod" value="hcs"/> |
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197 <param name="quick_block|pval" value="0.05"/> |
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198 <param name="quick_block|calcCiS" value="True"/> |
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199 <param name="quick_block|calcIso" value="False"/> |
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200 <param name="quick_block|calcCaS" value="False"/> |
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201 <param name="quick_block|multiplier" value="3"/> |
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202 <param name="options|option" value="show"/> |
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203 <param name="options|eicmax" value="200"/> |
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204 <param name="options|eicwidth" value="200"/> |
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205 <param name="options|value" value="into"/> |
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206 <param name="options|h" value="480"/> |
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207 <param name="options|w" value="640"/> |
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208 <param name="options|mzdec" value="2"/> |
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209 <param name="options|sortpval" value="False"/> |
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210 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> |
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211 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> |
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212 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> |
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213 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> |
| 0 | 214 </test> |
| 215 </tests> | |
| 216 | |
| 217 | |
| 218 | |
| 8 | 219 <help><![CDATA[ |
| 0 | 220 |
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221 @HELP_AUTHORS@ |
| 0 | 222 |
| 223 ================ | |
| 224 CAMERA.annotate | |
| 225 ================ | |
| 226 | |
| 227 ----------- | |
| 228 Description | |
| 229 ----------- | |
| 230 | |
| 231 The R-package CAMERA is a Collection of Algorithms for MEtabolite | |
| 232 pRofile Annotation. Its primary purpose is the annotation and evaluation of | |
| 233 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts | |
| 234 and fragments in peak lists. Additional methods cluster mass signals that | |
| 235 originate from a single metabolite, based on rules for mass differences and | |
| 236 peak shape comparison. To use the strength of already existing programs, | |
| 237 CAMERA is designed to interact directly with processed peak data from the | |
| 238 R-package **xcms**. | |
| 239 | |
| 240 **What it does?** | |
| 241 | |
| 242 The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). | |
| 243 | |
| 244 If you have two or more conditions, it will return a diffreport result within the annotation results. | |
| 245 The diffreport result shows the most significant differences between two sets of samples. Optionally | |
| 246 create extracted ion chromatograms for the most significant differences. | |
| 247 | |
| 248 | |
| 249 ----------------- | |
| 250 Workflow position | |
| 251 ----------------- | |
| 252 | |
| 253 | |
| 254 **Upstream tools** | |
| 255 | |
| 256 ========================= ==================== ====================== ========== | |
| 257 Name output file format parameter | |
| 258 ========================= ==================== ====================== ========== | |
| 259 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file | |
| 260 ========================= ==================== ====================== ========== | |
| 261 | |
| 262 | |
| 263 **Downstream tools** | |
| 264 | |
| 265 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 266 | Name | Output file | Format | | |
| 267 +===========================+=======================================+================================================+ | |
| 268 |CAMERA_combinexsAnnot |xset.annotate.dataMatrix.tsv | rdata.camera.positive or rdata.camera.negative | | |
| 269 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 270 |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular | | |
| 271 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 272 |Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular | | |
| 273 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 274 |Anova |xset.annotate.dataMatrix.tsv | Tabular | | |
| 275 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 276 |PCA |xset.annotate.dataMatrix.tsv | Tabular | | |
| 277 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 278 |Hierarchical Clustering |xset.annotate.dataMatrix.tsv | Tabular | | |
| 279 +---------------------------+---------------------------------------+------------------------------------------------+ | |
| 280 | |
| 281 | |
| 282 The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools: | |
| 283 | |
| 284 | Determine Vdk or Lowess | |
| 285 | Normalization Vdk/Lowess | |
| 286 | Anova | |
| 287 | PCA | |
| 288 | Hierarchical Clustering | |
| 289 | |
| 290 | |
| 291 **General schema of the metabolomic workflow** | |
| 292 | |
| 293 .. image:: annotate_workflow.png | |
| 294 | |
| 295 ----------- | |
| 296 Input files | |
| 297 ----------- | |
| 298 | |
| 299 +---------------------------+---------------------------+ | |
| 300 | Parameter : num + label | Format | | |
| 301 +===========================+===========================+ | |
| 302 | 1 : RData file | rdata.xcms.fillpeaks | | |
| 303 +---------------------------+---------------------------+ | |
| 304 | |
| 305 | |
| 306 ---------- | |
| 307 Parameters | |
| 308 ---------- | |
| 309 | |
| 310 diffreport: Intensity values to be used for the diffreport | |
| 311 ---------------------------------------------------------- | |
| 312 | |
| 313 | If **value="into"**, integrated peak intensities are used. | |
| 314 | If **value="maxo"**, maximum peak intensities are used. | |
| 315 | If **value="intb"**, baseline corrected integrated peak intensities are used (only available if peak detection was done by ‘findPeaks.centWave’). | |
| 316 | |
| 317 | |
| 318 | |
| 319 ------------ | |
| 320 Output files | |
| 321 ------------ | |
| 322 | |
| 323 xset.annotate.variableMetadata.tsv | |
| 324 | |
| 325 | For each metabolite (row) : | |
| 326 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup | |
| 327 | |
| 328 xset.annotate.dataMatrix.tsv | |
| 329 | |
| 330 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). | |
| 331 | |
| 332 xset.annotate.zip | |
| 333 | |
| 334 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). | |
| 335 | |
| 336 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative | |
| 337 | |
| 338 | Rdata file, that be used outside Galaxy in R. | |
| 339 | |
| 340 ------ | |
| 341 | |
| 342 .. class:: infomark | |
| 343 | |
| 344 The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: | |
| 345 | |
| 346 | Determine Vdk or Lowess (Data correction) | |
| 347 | Normalization Vdk/Lowess (Data correction) | |
| 348 | Anova (Statistical analysis) | |
| 349 | PCA (Statistical analysis) | |
| 350 | Hierarchical Clustering (Statistical analysis) | |
| 351 | |
| 352 | |
| 353 --------------------------------------------------- | |
| 354 | |
| 355 --------------- | |
| 356 Working example | |
| 357 --------------- | |
| 358 | |
| 359 Input files | |
| 360 ----------- | |
| 361 | |
| 362 | RData file -> **xset.fillPeaks.RData** | |
| 363 | |
| 364 Parameters | |
| 365 ---------- | |
| 366 | |
| 367 | sortpval -> **false** | |
| 368 | sigma -> **6 (default)** | |
| 369 | perfwhm -> **0.6 (default)** | |
| 370 | maxcharge -> **3 (default)** | |
| 371 | maxiso -> **4 (default)** | |
| 372 | minfrac -> **0.5 (default)** | |
| 373 | ppm -> **500** | |
| 374 | mzabs -> **0.015(default)** | |
| 375 | Advanced options -> **hide** | |
| 376 | Numver of condition -> Two or more conditioons | |
| 377 | eicmax -> **200** | |
| 378 | eicwidth -> **200 (default)** | |
| 379 | |
| 380 | |
| 381 | |
| 382 Output files | |
| 383 ------------ | |
| 384 | |
| 385 **Example of an xset.annotate.dataMatrix.tsv output** | |
| 386 | |
| 387 .. image:: annotatediffreport_dataMatrix.png | |
| 388 | |
| 389 **Example of a part of xset.annotate.variableMetadata.tsv output** | |
| 390 | |
| 391 .. image:: annotatediffreport_variableMetadata.png | |
| 392 | |
| 8 | 393 |
| 394 --------------------------------------------------- | |
| 395 | |
| 396 Changelog/News | |
| 397 -------------- | |
| 398 | |
|
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399 **Version 2.1.5 - 21/04/2016** |
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400 |
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401 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 |
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402 |
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403 |
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404 **Version 2.1.4 - 18/04/2016** |
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405 |
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406 - TEST: refactoring to pass planemo test using conda dependencies |
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407 |
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408 |
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409 **Version 2.1.3 - 10/02/2016** |
| 8 | 410 |
| 411 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
| 412 | |
| 413 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) | |
| 414 | |
| 415 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf. | |
| 416 | |
| 417 - UPDATE: refactoring of internal management of inputs/outputs | |
| 418 | |
| 419 | |
| 420 VERSION 2.1.0 - 09/10/2015** | |
| 421 | |
| 422 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) | |
| 423 | |
| 424 | |
| 425 VERSION 2.1.0 - 07/06/2015** | |
| 426 | |
| 427 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
| 428 | |
| 429 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
| 430 | |
| 431 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions | |
| 432 | |
| 433 | |
| 434 ]]></help> | |
| 0 | 435 |
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436 <expand macro="citation" /> |
| 0 | 437 |
| 438 | |
| 439 </tool> | |
| 440 | |
| 441 |