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