2
+ − 1 <tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="3">
+ − 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
+ − 21 </requirements>
+ − 22 <stdio>
+ − 23 <exit_code range="1:" level="fatal" />
+ − 24 </stdio>
+ − 25 <command>
+ − 26 <![CDATA[
+ − 27 Rscript
+ − 28 #if $technologies.technology == "Affymetrix":
+ − 29 '$__tool_directory__/Affymetrix_Preprocessing.R'
+ − 30 thefunctions "AffymetrixPreprocessingFunction"
+ − 31 path "pathtemp"
+ − 32 image $image
+ − 33 backgroundcorrection_method $technologies.BackgroundCorrectionA
+ − 34 normalization_method $technologies.NormalizationA
+ − 35 summary_method $technologies.SummarizationA
+ − 36 #elif $technologies.technology == "Agilent":
+ − 37 #if $technologies.channelsA.channelA == "one":
+ − 38 '$__tool_directory__/Agilent_One_Color_Preprocessing.R'
+ − 39 thefunction "AgilentOneColorPreprocessingFunction"
+ − 40 path "pathtemp"
+ − 41 image $image
+ − 42 methodBC $technologies.channelsA.BackgroundCorrectionAG
+ − 43 methodNBA $technologies.channelsA.methodNBAAG
+ − 44 #else:
+ − 45 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R'
+ − 46 thefunction "AgilentTwoChannelsPreprocessingFunction"
+ − 47 path "pathtemp"
+ − 48 image $image
+ − 49 methodBC $technologies.channelsA.BackgroundCorrectionAGT
+ − 50 methodNWA $technologies.channelsA.methodNWAAGT
+ − 51 methodNBA $technologies.channelsA.methodNBAAGT
+ − 52 #end if
+ − 53 #else:
+ − 54 #if $technologies.channelsG.channelG == "one"
+ − 55 '$__tool_directory__/GenePix_One_Color_Preprocessing.R'
+ − 56 thefunction "GenePixOneColorPreprocessingFunction"
+ − 57 path "pathtemp"
+ − 58 image $image
+ − 59 methodBC $technologies.channelsG.BackgroundCorrectionG
+ − 60 methodNBA $technologies.channelsG.methodNBAG
+ − 61 #else:
+ − 62 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R'
+ − 63 thefunction "GenePixTwoChannelsPreprocessingFunction"
+ − 64 path "pathtemp"
+ − 65 image $image
+ − 66 methodBC $technologies.channelsG.BackgroundCorrectionGT
+ − 67 methodNWA $technologies.channelsG.methodNWAGT
+ − 68 methodNBA $technologies.channelsG.methodNBAGT
+ − 69 #end if
+ − 70 #end if
+ − 71 w $w
+ − 72 h $h
+ − 73 ]]>
+ − 74 </command>
+ − 75 <inputs>
+ − 76 <param name="image" type="data" format="rdata" label="Project microarray as a binary rdata" help="Last output from tool read dataset." >
+ − 77 <validator type="expression" message="Please select output dataset from read dataset tool ">'Read.Project' in value.name</validator>
+ − 78 </param>
+ − 79 <conditional name="technologies">
+ − 80 <param name="technology" type="select" label="Select the technology">
+ − 81 <option value="Affymetrix" selected="true">Affymetrix</option>
+ − 82 <option value="Agilent">Agilent</option>
+ − 83 <option value="GenePix">GenePix</option>
+ − 84 </param>
+ − 85 <when value="Affymetrix">
+ − 86 <param name="BackgroundCorrectionA" type="select" label="Background correction method.">
+ − 87 <option value="mas" selected="true">Mas</option>
+ − 88 <option value="rma">Rma</option>
+ − 89 <option value="none">None</option>
+ − 90 </param>
+ − 91 <param name="NormalizationA" type="select" label="Normalization method.">
+ − 92 <option value="quantiles" selected="true">Quantiles</option>
+ − 93 <option value="quantiles.robust">Quantiles robust</option>
+ − 94 <option value="quantiles.probeset">Quantiles Probeset</option>
+ − 95 <option value="constant">Constant</option>
+ − 96 <option value="contrasts">Contrasts</option>
+ − 97 <option value="invariantset">Invariantset</option>
+ − 98 <option value="loess">Loess</option>
+ − 99 <option value="qspline">QSPline</option>
+ − 100 <option value="scaling">Scaling</option>
+ − 101 <option value="vsn">VSN</option>
+ − 102 </param>
+ − 103 <param name="SummarizationA" type="select" label="Summarization method.">
+ − 104 <option value="median.polish" selected="true">Median.polish</option>
+ − 105 <option value="tukey.biweight">Tukey.biweight</option>
+ − 106 <option value="average.log">Average.log</option>
+ − 107 <option value="log.average">Log.average</option>
+ − 108 <option value="rlm">Rlm</option>
+ − 109 <option value="lm">Lm</option>
+ − 110 <option value="log.median">Log.median</option>
+ − 111 <option value="median.log">Median.log</option>
+ − 112 <option value="log.2nd.largest">Log.2nd.largest</option>
+ − 113 </param>
+ − 114 </when>
+ − 115 <when value="Agilent">
+ − 116 <conditional name="channelsA">
+ − 117 <param name="channelA" type="select" label="Select the number of channels">
+ − 118 <option value="one" selected="true">One</option>
+ − 119 <option value="two">Two</option>
+ − 120 </param>
+ − 121 <when value="one">
+ − 122 <param name="BackgroundCorrectionAG" type="select" label="Background correction method.">
+ − 123 <option value="auto" selected="true">Auto</option>
+ − 124 <option value="none">None</option>
+ − 125 <option value="subtract">Subtract</option>
+ − 126 <option value="half">Half</option>
+ − 127 <option value="minimum">Minimum</option>
+ − 128 <option value="movingmin">MovingMin</option>
+ − 129 <option value="edwards">Edwards</option>
+ − 130 <option value="normexp">NormExp</option>
+ − 131 </param>
+ − 132 <param name="methodNBAAG" type="select" label="Normalization between arrays.">
+ − 133 <option value="scale" selected="true">Scale</option>
+ − 134 <option value="quantile">Quantile</option>
+ − 135 <option value="cyclicloess">CyclicLoess</option>
+ − 136 </param>
+ − 137 </when>
+ − 138 <when value="two">
+ − 139 <param name="BackgroundCorrectionAGT" type="select" label="Background correction method.">
+ − 140 <option value="auto" selected="true">Auto</option>
+ − 141 <option value="none">None</option>
+ − 142 <option value="subtract">Subtract</option>
+ − 143 <option value="half">Half</option>
+ − 144 <option value="minimum">Minimum</option>
+ − 145 <option value="movingmin">MovingMin</option>
+ − 146 <option value="edwards">Edwards</option>
+ − 147 <option value="normexp">NormExp</option>
+ − 148 </param>
+ − 149 <param name="methodNWAAGT" type="select" label="Normalization within arrays.">
+ − 150 <option value="median" selected="true">Median</option>
+ − 151 <option value="loess">Loess</option>
+ − 152 <option value="printtiploess">PrintTiploess</option>
+ − 153 </param>
+ − 154 <param name="methodNBAAGT" type="select" label="Normalization between arrays.">
+ − 155 <option value="scale" selected="true">Scale</option>
+ − 156 <option value="quantile">Quantile</option>
+ − 157 <option value="Aquantile">AQuantile</option>
+ − 158 <option value="cyclicloess">CyclicLoess</option>
+ − 159 </param>
+ − 160 </when>
+ − 161 </conditional>
+ − 162 </when>
+ − 163 <when value="GenePix">
+ − 164 <conditional name="channelsG">
+ − 165 <param name="channelG" type="select" label="Select the number of channels">
+ − 166 <option value="one" selected="true">One</option>
+ − 167 <option value="two">Two</option>
+ − 168 </param>
+ − 169 <when value="one">
+ − 170 <param name="BackgroundCorrectionG" type="select" label="Background correction method.">
+ − 171 <option value="auto" selected="true">Auto</option>
+ − 172 <option value="none">None</option>
+ − 173 <option value="subtract">Subtract</option>
+ − 174 <option value="half">Half</option>
+ − 175 <option value="minimum">Minimum</option>
+ − 176 <option value="movingmin">MovingMin</option>
+ − 177 <option value="edwards">Edwards</option>
+ − 178 <option value="normexp">NormExp</option>
+ − 179 </param>
+ − 180 <param name="methodNBAG" type="select" label="Normalization between arrays.">
+ − 181 <!--<option value="scale" selected="true">Scale</option>-->
+ − 182 <option value="quantile" selected="true">Quantile</option>
+ − 183 <option value="scale">Scale</option>
+ − 184 <option value="cyclicloess">CyclicLoess</option>
+ − 185 </param>
+ − 186 </when>
+ − 187 <when value="two">
+ − 188 <param name="BackgroundCorrectionGT" type="select" label="Background correction method.">
+ − 189 <option value="auto" selected="true">Auto</option>
+ − 190 <option value="none">None</option>
+ − 191 <option value="subtract">Subtract</option>
+ − 192 <option value="half">Half</option>
+ − 193 <option value="minimum">Minimum</option>
+ − 194 <option value="movingmin">MovingMin</option>
+ − 195 <option value="edwards">Edwards</option>
+ − 196 <option value="normexp">NormExp</option>
+ − 197 </param>
+ − 198 <param name="methodNWAGT" type="select" label="Normalization within arrays.">
+ − 199 <option value="median" selected="true">Median</option>
+ − 200 <option value="loess">Loess</option>
+ − 201 <option value="printtiploess">PrintTiploess</option>
+ − 202 </param>
+ − 203 <param name="methodNBAGT" type="select" label="Normalization between arrays.">
+ − 204 <!--<option value="scale" >Scale</option>-->
+ − 205 <option value="quantile" selected="true">Quantile</option>
+ − 206 <option value="scale">Scale</option>
+ − 207 <option value="cyclicloess">CyclicLoess</option>
+ − 208 <option value="Aquantile">AQuantile</option>
+ − 209 </param>
+ − 210 </when>
+ − 211 </conditional>
+ − 212 </when>
+ − 213 </conditional>
+ − 214 <param name="w" type="integer" value="1024" label="Plot's width" />
+ − 215 <param name="h" type="integer" value="1024" label="Plot's height" />
+ − 216 </inputs>
+ − 217 <outputs>
+ − 218 <data name="ProcessDataSetRData" format="rdata" from_work_dir="MicroArray.Preprocessing.RData" label="Preprocess.Project.Data.RData" />
+ − 219 <data name="Matrix.Data" format="tabular" from_work_dir="Matrix.Data.tsv" label="Matrix.Data.tsv" />
+ − 220 <data name="Preprocessing.Plots" format="html" from_work_dir="PreprocessingPlots.html" label="Preprocessing.Plots.html" />
+ − 221 </outputs>
+ − 222 <tests>
+ − 223 <test>
+ − 224 <param name="image" ftype="rdata" value="Read.Project.Data.RData" />
+ − 225 <param name="technologies|technology" value="GenePix"/>
+ − 226 <param name="technologies|channelsG|channelG" value="two"/>
+ − 227 <param name="technologies|channelsG|BackgroundCorrectionGT" value="auto"/>
+ − 228 <param name="technologies|channelsG|methodNWAGT" value="median"/>
+ − 229 <param name="technologies|channelsG|methodNBAGT" value="quantile"/>
+ − 230 <output name="ProcessDataSetRData" ftype="rdata" file="Preprocess.Project.Data.RData" compare="sim_size" >
+ − 231 </output>
+ − 232 <output name="Matrix.Data" ftype="tabular" file="Matrix.Data.tsv" >
+ − 233 </output>
+ − 234 <output name="Preprocessing.Plots" ftype="html" file="Preprocessing.Plots.html" compare="sim_size">
+ − 235 </output>
+ − 236 </test>
+ − 237 </tests>
+ − 238 <help>
+ − 239
+ − 240 .. class:: infomark
+ − 241
+ − 242 **Authors** T.Bensellak, B.Ettetuani.
+ − 243
+ − 244 ---------------------------------------------------
+ − 245
+ − 246 ==================================
+ − 247 Preprocessing Microarray DataSet
+ − 248 ==================================
+ − 249
+ − 250 -----------
+ − 251 Description
+ − 252 -----------
+ − 253
+ − 254 This tool is used as first phase of the global workflow, the preprocessing .
+ − 255
+ − 256 -----------------
+ − 257 Workflow position
+ − 258 -----------------
+ − 259
+ − 260 **Upstream tools**
+ − 261
+ − 262 +-------------------------------+------------------------------+---------+
+ − 263 | Name | output file |format |
+ − 264 +===============================+==============================+=========+
+ − 265 | Read.DataSet.Microarray | MicroArrayObject.RData | Rdat |
+ − 266 +-------------------------------+------------------------------+---------+
+ − 267
+ − 268
+ − 269 **Downstream tools**
+ − 270
+ − 271 +-----------------------------------------------+----------------------------------------------+---------+
+ − 272 | Name | Output file | Format |
+ − 273 +===============================================+==============================================+=========+
+ − 274 |Tests and Selection | Test.results.tsv | Tabular |
+ − 275 +-----------------------------------------------+----------------------------------------------+---------+
+ − 276
+ − 277 -----------
+ − 278 Input files
+ − 279 -----------
+ − 280
+ − 281 +---------------------------+------------+
+ − 282 | Parameter : num + label | Format |
+ − 283 +===========================+============+
+ − 284 | Image | Rdata |
+ − 285 +---------------------------+------------+
+ − 286 | Methods parmeters | Numeric |
+ − 287 +---------------------------+------------+
+ − 288
+ − 289 ------------
+ − 290 Output files
+ − 291 ------------
+ − 292
+ − 293 **Microarray.Preprocessing.RData**
+ − 294
+ − 295 **Matrix.Data.tsv**
+ − 296
+ − 297 ------------------------------
+ − 298 General schema of the workflow
+ − 299 ------------------------------
+ − 300
+ − 301 https://bensellak.github.io/microarrays-galaxy/workflow.png
+ − 302
+ − 303
+ − 304 </help>
+ − 305 <expand macro="R_citation">
+ − 306 </expand>
+ − 307 </tool>
