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comparison preprocess_datasets/Preprocess_DataSet.xml @ 11:bdc430a41508 draft

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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>