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