Mercurial > repos > proteomisc > preprocess_dataset
comparison preprocess_datasets/Preprocess_DataSet.xml @ 11:bdc430a41508 draft
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| author | proteomisc |
|---|---|
| date | Sun, 03 Dec 2023 14:07:23 +0000 |
| parents | |
| children | a847ef7aa259 |
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| 10:09a8947f1031 | 11:bdc430a41508 |
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| 1 <tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="4"> | |
| 2 <description> Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization. </description> | |
| 3 <macros> | |
| 4 <import>citations.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <requirement type="package">r-base</requirement> | |
| 8 <requirement type="package">r-batch</requirement> | |
| 9 <requirement type="package">bioconductor-affyplm</requirement> | |
| 10 <requirement type="package">bioconductor-affy</requirement> | |
| 11 <requirement type="package">bioconductor-annotate</requirement> | |
| 12 <requirement type="package">r-knitr</requirement> | |
| 13 <requirement type="package">bioconductor-marray</requirement> | |
| 14 <requirement type="package">r-idpmisc</requirement> | |
| 15 <requirement type="package">r-kernsmooth</requirement> | |
| 16 <requirement type="package">r-rmarkdown</requirement> | |
| 17 <requirement type="package">r-markdown</requirement> | |
| 18 <requirement type="package">bioconductor-limma</requirement> | |
| 19 <requirement type="package">r-idpmisc</requirement> | |
| 20 </requirements> | |
| 21 <stdio> | |
| 22 <exit_code range="1:" level="fatal" /> | |
| 23 </stdio> | |
| 24 <command> | |
| 25 <![CDATA[ | |
| 26 Rscript | |
| 27 #if $technologies.technology == "Affymetrix": | |
| 28 '$__tool_directory__/Affymetrix_Preprocessing.R' | |
| 29 thefunctions "AffymetrixPreprocessingFunction" | |
| 30 path "pathtemp" | |
| 31 image $image | |
| 32 backgroundcorrection_method $technologies.BackgroundCorrectionA | |
| 33 normalization_method $technologies.NormalizationA | |
| 34 summary_method $technologies.SummarizationA | |
| 35 #elif $technologies.technology == "Agilent": | |
| 36 #if $technologies.channelsA.channelA == "one": | |
| 37 '$__tool_directory__/Agilent_One_Color_Preprocessing.R' | |
| 38 thefunction "AgilentOneColorPreprocessingFunction" | |
| 39 path "pathtemp" | |
| 40 image $image | |
| 41 methodBC $technologies.channelsA.BackgroundCorrectionAG | |
| 42 methodNBA $technologies.channelsA.methodNBAAG | |
| 43 #else: | |
| 44 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R' | |
| 45 thefunction "AgilentTwoChannelsPreprocessingFunction" | |
| 46 path "pathtemp" | |
| 47 image $image | |
| 48 methodBC $technologies.channelsA.BackgroundCorrectionAGT | |
| 49 methodNWA $technologies.channelsA.methodNWAAGT | |
| 50 methodNBA $technologies.channelsA.methodNBAAGT | |
| 51 #end if | |
| 52 #else: | |
| 53 #if $technologies.channelsG.channelG == "one" | |
| 54 '$__tool_directory__/GenePix_One_Color_Preprocessing.R' | |
| 55 thefunction "GenePixOneColorPreprocessingFunction" | |
| 56 path "pathtemp" | |
| 57 image $image | |
| 58 methodBC $technologies.channelsG.BackgroundCorrectionG | |
| 59 methodNBA $technologies.channelsG.methodNBAG | |
| 60 #else: | |
| 61 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R' | |
| 62 thefunction "GenePixTwoChannelsPreprocessingFunction" | |
| 63 path "pathtemp" | |
| 64 image $image | |
| 65 methodBC $technologies.channelsG.BackgroundCorrectionGT | |
| 66 methodNWA $technologies.channelsG.methodNWAGT | |
| 67 methodNBA $technologies.channelsG.methodNBAGT | |
| 68 #end if | |
| 69 #end if | |
| 70 w $w | |
| 71 h $h | |
| 72 ]]> | |
| 73 </command> | |
| 74 <inputs> | |
| 75 <param name="image" type="data" format="rdata" label="Project microarray as a binary rdata" help="Last output from tool read dataset." > | |
| 76 <validator type="expression" message="Please select output dataset from read dataset tool ">'Read.Project' in value.name</validator> | |
| 77 </param> | |
| 78 <conditional name="technologies"> | |
| 79 <param name="technology" type="select" label="Select the technology"> | |
| 80 <option value="Affymetrix" selected="true">Affymetrix</option> | |
| 81 <option value="Agilent">Agilent</option> | |
| 82 <option value="GenePix">GenePix</option> | |
| 83 </param> | |
| 84 <when value="Affymetrix"> | |
| 85 <param name="BackgroundCorrectionA" type="select" label="Background correction method."> | |
| 86 <option value="mas" selected="true">Mas</option> | |
| 87 <option value="rma">Rma</option> | |
| 88 <option value="none">None</option> | |
| 89 </param> | |
| 90 <param name="NormalizationA" type="select" label="Normalization method."> | |
| 91 <option value="quantiles" selected="true">Quantiles</option> | |
| 92 <option value="quantiles.robust">Quantiles robust</option> | |
| 93 <option value="quantiles.probeset">Quantiles Probeset</option> | |
| 94 <option value="constant">Constant</option> | |
| 95 <option value="contrasts">Contrasts</option> | |
| 96 <option value="invariantset">Invariantset</option> | |
| 97 <option value="loess">Loess</option> | |
| 98 <option value="qspline">QSPline</option> | |
| 99 <option value="scaling">Scaling</option> | |
| 100 <option value="vsn">VSN</option> | |
| 101 </param> | |
| 102 <param name="SummarizationA" type="select" label="Summarization method."> | |
| 103 <option value="median.polish" selected="true">Median.polish</option> | |
| 104 <option value="tukey.biweight">Tukey.biweight</option> | |
| 105 <option value="average.log">Average.log</option> | |
| 106 <option value="log.average">Log.average</option> | |
| 107 <option value="rlm">Rlm</option> | |
| 108 <option value="lm">Lm</option> | |
| 109 <option value="log.median">Log.median</option> | |
| 110 <option value="median.log">Median.log</option> | |
| 111 <option value="log.2nd.largest">Log.2nd.largest</option> | |
| 112 </param> | |
| 113 </when> | |
| 114 <when value="Agilent"> | |
| 115 <conditional name="channelsA"> | |
| 116 <param name="channelA" type="select" label="Select the number of channels"> | |
| 117 <option value="one" selected="true">One</option> | |
| 118 <option value="two">Two</option> | |
| 119 </param> | |
| 120 <when value="one"> | |
| 121 <param name="BackgroundCorrectionAG" type="select" label="Background correction method."> | |
| 122 <option value="auto" selected="true">Auto</option> | |
| 123 <option value="none">None</option> | |
| 124 <option value="subtract">Subtract</option> | |
| 125 <option value="half">Half</option> | |
| 126 <option value="minimum">Minimum</option> | |
| 127 <option value="movingmin">MovingMin</option> | |
| 128 <option value="edwards">Edwards</option> | |
| 129 <option value="normexp">NormExp</option> | |
| 130 </param> | |
| 131 <param name="methodNBAAG" type="select" label="Normalization between arrays."> | |
| 132 <option value="scale" selected="true">Scale</option> | |
| 133 <option value="quantile">Quantile</option> | |
| 134 <option value="cyclicloess">CyclicLoess</option> | |
| 135 </param> | |
| 136 </when> | |
| 137 <when value="two"> | |
| 138 <param name="BackgroundCorrectionAGT" type="select" label="Background correction method."> | |
| 139 <option value="auto" selected="true">Auto</option> | |
| 140 <option value="none">None</option> | |
| 141 <option value="subtract">Subtract</option> | |
| 142 <option value="half">Half</option> | |
| 143 <option value="minimum">Minimum</option> | |
| 144 <option value="movingmin">MovingMin</option> | |
| 145 <option value="edwards">Edwards</option> | |
| 146 <option value="normexp">NormExp</option> | |
| 147 </param> | |
| 148 <param name="methodNWAAGT" type="select" label="Normalization within arrays."> | |
| 149 <option value="median" selected="true">Median</option> | |
| 150 <option value="loess">Loess</option> | |
| 151 <option value="printtiploess">PrintTiploess</option> | |
| 152 </param> | |
| 153 <param name="methodNBAAGT" type="select" label="Normalization between arrays."> | |
| 154 <option value="scale" selected="true">Scale</option> | |
| 155 <option value="quantile">Quantile</option> | |
| 156 <option value="Aquantile">AQuantile</option> | |
| 157 <option value="cyclicloess">CyclicLoess</option> | |
| 158 </param> | |
| 159 </when> | |
| 160 </conditional> | |
| 161 </when> | |
| 162 <when value="GenePix"> | |
| 163 <conditional name="channelsG"> | |
| 164 <param name="channelG" type="select" label="Select the number of channels"> | |
| 165 <option value="one" selected="true">One</option> | |
| 166 <option value="two">Two</option> | |
| 167 </param> | |
| 168 <when value="one"> | |
| 169 <param name="BackgroundCorrectionG" type="select" label="Background correction method."> | |
| 170 <option value="auto" selected="true">Auto</option> | |
| 171 <option value="none">None</option> | |
| 172 <option value="subtract">Subtract</option> | |
| 173 <option value="half">Half</option> | |
| 174 <option value="minimum">Minimum</option> | |
| 175 <option value="movingmin">MovingMin</option> | |
| 176 <option value="edwards">Edwards</option> | |
| 177 <option value="normexp">NormExp</option> | |
| 178 </param> | |
| 179 <param name="methodNBAG" type="select" label="Normalization between arrays."> | |
| 180 <!--<option value="scale" selected="true">Scale</option>--> | |
| 181 <option value="quantile" selected="true">Quantile</option> | |
| 182 <option value="scale">Scale</option> | |
| 183 <option value="cyclicloess">CyclicLoess</option> | |
| 184 </param> | |
| 185 </when> | |
| 186 <when value="two"> | |
| 187 <param name="BackgroundCorrectionGT" type="select" label="Background correction method."> | |
| 188 <option value="auto" selected="true">Auto</option> | |
| 189 <option value="none">None</option> | |
| 190 <option value="subtract">Subtract</option> | |
| 191 <option value="half">Half</option> | |
| 192 <option value="minimum">Minimum</option> | |
| 193 <option value="movingmin">MovingMin</option> | |
| 194 <option value="edwards">Edwards</option> | |
| 195 <option value="normexp">NormExp</option> | |
| 196 </param> | |
| 197 <param name="methodNWAGT" type="select" label="Normalization within arrays."> | |
| 198 <option value="median" selected="true">Median</option> | |
| 199 <option value="loess">Loess</option> | |
| 200 <option value="printtiploess">PrintTiploess</option> | |
| 201 </param> | |
| 202 <param name="methodNBAGT" type="select" label="Normalization between arrays."> | |
| 203 <!--<option value="scale" >Scale</option>--> | |
| 204 <option value="quantile" selected="true">Quantile</option> | |
| 205 <option value="scale">Scale</option> | |
| 206 <option value="cyclicloess">CyclicLoess</option> | |
| 207 <option value="Aquantile">AQuantile</option> | |
| 208 </param> | |
| 209 </when> | |
| 210 </conditional> | |
| 211 </when> | |
| 212 </conditional> | |
| 213 <param name="w" type="integer" value="1024" label="Plot's width" /> | |
| 214 <param name="h" type="integer" value="1024" label="Plot's height" /> | |
| 215 </inputs> | |
| 216 <outputs> | |
| 217 <data name="ProcessDataSetRData" format="rdata" from_work_dir="MicroArray.Preprocessing.RData" label="Preprocess.Project.Data.RData" /> | |
| 218 <data name="Matrix.Data" format="tabular" from_work_dir="Matrix.Data.tsv" label="Matrix.Data.tsv" /> | |
| 219 <data name="Preprocessing.Plots" format="html" from_work_dir="PreprocessingPlots.html" label="Preprocessing.Plots.html" /> | |
| 220 </outputs> | |
| 221 <tests> | |
| 222 <test> | |
| 223 <param name="image" ftype="rdata" value="Read.Project.Data.RData" /> | |
| 224 <param name="technologies|technology" value="GenePix"/> | |
| 225 <param name="technologies|channelsG|channelG" value="two"/> | |
| 226 <param name="technologies|channelsG|BackgroundCorrectionGT" value="auto"/> | |
| 227 <param name="technologies|channelsG|methodNWAGT" value="median"/> | |
| 228 <param name="technologies|channelsG|methodNBAGT" value="quantile"/> | |
| 229 <output name="ProcessDataSetRData" ftype="rdata" file="Preprocess.Project.Data.RData" compare="sim_size" > | |
| 230 </output> | |
| 231 <output name="Matrix.Data" ftype="tabular" file="Matrix.Data.tsv" > | |
| 232 </output> | |
| 233 <output name="Preprocessing.Plots" ftype="html" file="Preprocessing.Plots.html" compare="sim_size"> | |
| 234 </output> | |
| 235 </test> | |
| 236 </tests> | |
| 237 <help> | |
| 238 | |
| 239 .. class:: infomark | |
| 240 | |
| 241 **Authors** T.Bensellak, B.Ettetuani. | |
| 242 | |
| 243 --------------------------------------------------- | |
| 244 | |
| 245 ================================== | |
| 246 Preprocessing Microarray DataSet | |
| 247 ================================== | |
| 248 | |
| 249 ----------- | |
| 250 Description | |
| 251 ----------- | |
| 252 | |
| 253 This tool is used as first phase of the global workflow, the preprocessing . | |
| 254 | |
| 255 ----------------- | |
| 256 Workflow position | |
| 257 ----------------- | |
| 258 | |
| 259 **Upstream tools** | |
| 260 | |
| 261 +-------------------------------+------------------------------+---------+ | |
| 262 | Name | output file |format | | |
| 263 +===============================+==============================+=========+ | |
| 264 | Read.DataSet.Microarray | MicroArrayObject.RData | Rdat | | |
| 265 +-------------------------------+------------------------------+---------+ | |
| 266 | |
| 267 | |
| 268 **Downstream tools** | |
| 269 | |
| 270 +-----------------------------------------------+----------------------------------------------+---------+ | |
| 271 | Name | Output file | Format | | |
| 272 +===============================================+==============================================+=========+ | |
| 273 |Tests and Selection | Test.results.tsv | Tabular | | |
| 274 +-----------------------------------------------+----------------------------------------------+---------+ | |
| 275 | |
| 276 ----------- | |
| 277 Input files | |
| 278 ----------- | |
| 279 | |
| 280 +---------------------------+------------+ | |
| 281 | Parameter : num + label | Format | | |
| 282 +===========================+============+ | |
| 283 | Image | Rdata | | |
| 284 +---------------------------+------------+ | |
| 285 | Methods parmeters | Numeric | | |
| 286 +---------------------------+------------+ | |
| 287 | |
| 288 ------------ | |
| 289 Output files | |
| 290 ------------ | |
| 291 | |
| 292 **Microarray.Preprocessing.RData** | |
| 293 | |
| 294 **Matrix.Data.tsv** | |
| 295 | |
| 296 ------------------------------ | |
| 297 General schema of the workflow | |
| 298 ------------------------------ | |
| 299 | |
| 300 https://bensellak.github.io/microarrays-galaxy/workflow.png | |
| 301 | |
| 302 | |
| 303 </help> | |
| 304 <expand macro="R_citation"> | |
| 305 </expand> | |
| 306 </tool> |