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