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comparison preprocess_datasets/test-data/Preprocess_DataSet.xml @ 2:575cf0e82cab draft

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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>