DocBookSupport: raw_data_importer_genepix-cy3_cy5.xml

File raw_data_importer_genepix-cy3_cy5.xml, 8.9 KB (added by Jari Häkkinen, 16 years ago)
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd">
3<!--
4 Copyright (C) 2007 Jari Hakkinen, Martin Svensson
5
6 This file is part of BASE - BioArray Software Environment.
7 Available at http://base.thep.lu.se/
8
9 BASE is free software; you can redistribute it and/or modify it
10 under the terms of the GNU General Public License as published by
11 the Free Software Foundation; either version 3 of the License, or
12 (at your option) any later version.
13
14 BASE is distributed in the hope that it will be useful, but WITHOUT
15 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
16 or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
17 License for more details.
18
19 You should have received a copy of the GNU General Public License
20 along with BASE. If not, see <http://www.gnu.org/licenses/>.
21-->
22<configfile>
23 <configuration pluginClassName="net.sf.basedb.plugins.RawDataFlatFileImporter">
24 <configname>GenePix raw data import (cy3/cy5)</configname>
25 <description>Configuration to import raw data from a genepix file(*.gpr).&#xD;
26The wavelengths should be 532nm for channel_1 and 635nm for channel_2.</description>
27 <parameter>
28 <name>yColumnMapping</name>
29 <label>Y</label>
30 <description />
31 <class>java.lang.String</class>
32 <value>\Y\</value>
33 </parameter>
34 <parameter>
35 <name>propertyMapping.ch2BgMean</name>
36 <label>Channel 2 background mean</label>
37 <description />
38 <class>java.lang.String</class>
39 <value>\B635 Mean\</value>
40 </parameter>
41 <parameter>
42 <name>propertyMapping.flags</name>
43 <label>Flags</label>
44 <description />
45 <class>java.lang.String</class>
46 <value>\Flags\</value>
47 </parameter>
48 <parameter>
49 <name>propertyMapping.mValue</name>
50 <label>M value</label>
51 <description />
52 <class>java.lang.String</class>
53 <value>\Log Ratio (532/635)\</value>
54 </parameter>
55 <parameter>
56 <name>trimQuotes</name>
57 <label>Remove quotes</label>
58 <description />
59 <class>java.lang.Boolean</class>
60 <value>true</value>
61 </parameter>
62 <parameter>
63 <name>propertyMapping.diameter</name>
64 <label>Spot diameter</label>
65 <description />
66 <class>java.lang.String</class>
67 <value>\Dia.\</value>
68 </parameter>
69 <parameter>
70 <name>propertyMapping.ch2PercSat</name>
71 <label>Percent saturated pixels</label>
72 <description />
73 <class>java.lang.String</class>
74 <value>\F635 % Sat.\</value>
75 </parameter>
76 <parameter>
77 <name>propertyMapping.ch1FgSd</name>
78 <label>Channel 1 foreground standard deviation</label>
79 <description />
80 <class>java.lang.String</class>
81 <value>\F532 SD\</value>
82 </parameter>
83 <parameter>
84 <name>propertyMapping.ch2PercSd1</name>
85 <label>Percent pixels within 1 standard deviation</label>
86 <description />
87 <class>java.lang.String</class>
88 <value>\% &gt; B635+1SD\</value>
89 </parameter>
90 <parameter>
91 <name>propertyMapping.fgPixels</name>
92 <label>Foreground pixels</label>
93 <description />
94 <class>java.lang.String</class>
95 <value>\F Pixels\</value>
96 </parameter>
97 <parameter>
98 <name>propertyMapping.ch2FgSd</name>
99 <label>Channel 2 foreground standard deviation</label>
100 <description />
101 <class>java.lang.String</class>
102 <value>\F635 SD\</value>
103 </parameter>
104 <parameter>
105 <name>propertyMapping.ch2BgSd</name>
106 <label>Channel 2 background standard deviation</label>
107 <description />
108 <class>java.lang.String</class>
109 <value>\B635 SD\</value>
110 </parameter>
111 <parameter>
112 <name>headerRegexp</name>
113 <label>Header</label>
114 <description />
115 <class>java.lang.String</class>
116 <value>"(.+)=(.*)"</value>
117 </parameter>
118 <parameter>
119 <name>reporterIdColumnMapping</name>
120 <label>Reporter ID</label>
121 <description />
122 <class>java.lang.String</class>
123 <value>\ID\</value>
124 </parameter>
125 <parameter>
126 <name>propertyMapping.ch1FgMedian</name>
127 <label>Channel 1 foreground median</label>
128 <description />
129 <class>java.lang.String</class>
130 <value>\F532 Median\</value>
131 </parameter>
132 <parameter>
133 <name>propertyMapping.ch1BgMean</name>
134 <label>Channel 1 background mean</label>
135 <description />
136 <class>java.lang.String</class>
137 <value>\B532 Mean\</value>
138 </parameter>
139 <parameter>
140 <name>propertyMapping.ch2BgMedian</name>
141 <label>Channel 2 background median</label>
142 <description />
143 <class>java.lang.String</class>
144 <value>\B635 Median\</value>
145 </parameter>
146 <parameter>
147 <name>rowColumnMapping</name>
148 <label>Row</label>
149 <description />
150 <class>java.lang.String</class>
151 <value>\Row\</value>
152 </parameter>
153 <parameter>
154 <name>propertyMapping.ch1BgMedian</name>
155 <label>Channel 1 background median</label>
156 <description />
157 <class>java.lang.String</class>
158 <value>\B532 Median\</value>
159 </parameter>
160 <parameter>
161 <name>propertyMapping.ch2FgMean</name>
162 <label>Channel 2 foreground mean</label>
163 <description />
164 <class>java.lang.String</class>
165 <value>\F635 Mean\</value>
166 </parameter>
167 <parameter>
168 <name>propertyMapping.rgnR2</name>
169 <label>Rgn R2</label>
170 <description />
171 <class>java.lang.String</class>
172 <value>\Rgn R² (532/635)\</value>
173 </parameter>
174 <parameter>
175 <name>dataHeaderRegexp</name>
176 <label>Data header</label>
177 <description />
178 <class>java.lang.String</class>
179 <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*</value>
180 </parameter>
181 <parameter>
182 <name>propertyMapping.ratiosSd</name>
183 <label>Standard deviation of ratios</label>
184 <description />
185 <class>java.lang.String</class>
186 <value>\Ratios SD (532/635)\</value>
187 </parameter>
188 <parameter>
189 <name>propertyMapping.ch2FgMedian</name>
190 <label>Channel 2 foreground median</label>
191 <description />
192 <class>java.lang.String</class>
193 <value>\F635 Median\</value>
194 </parameter>
195 <parameter>
196 <name>propertyMapping.ch1PercSat</name>
197 <label>Percent saturated pixels</label>
198 <description />
199 <class>java.lang.String</class>
200 <value>\F532 % Sat.\</value>
201 </parameter>
202 <parameter>
203 <name>dataSplitterRegexp</name>
204 <label>Data splitter</label>
205 <description />
206 <class>java.lang.String</class>
207 <value>\t</value>
208 </parameter>
209 <parameter>
210 <name>columnColumnMapping</name>
211 <label>Column</label>
212 <description />
213 <class>java.lang.String</class>
214 <value>\Column\</value>
215 </parameter>
216 <parameter>
217 <name>propertyMapping.bgPixels</name>
218 <label>Background pixels</label>
219 <description />
220 <class>java.lang.String</class>
221 <value>\B Pixels\</value>
222 </parameter>
223 <parameter>
224 <name>propertyMapping.ch1PercSd2</name>
225 <label>Percent pixels within 2 standard deviations</label>
226 <description />
227 <class>java.lang.String</class>
228 <value>\% &gt; B532+2SD\</value>
229 </parameter>
230 <parameter>
231 <name>propertyMapping.ch1FgMean</name>
232 <label>Channel 1 foreground mean</label>
233 <description />
234 <class>java.lang.String</class>
235 <value>\F532 Mean\</value>
236 </parameter>
237 <parameter>
238 <name>xColumnMapping</name>
239 <label>X</label>
240 <description />
241 <class>java.lang.String</class>
242 <value>\X\</value>
243 </parameter>
244 <parameter>
245 <name>propertyMapping.ch1BgSd</name>
246 <label>Channel 1 background standard deviation</label>
247 <description />
248 <class>java.lang.String</class>
249 <value>\B532 SD\</value>
250 </parameter>
251 <parameter>
252 <name>propertyMapping.rgnRatio</name>
253 <label>Rgn ratio</label>
254 <description />
255 <class>java.lang.String</class>
256 <value>\Rgn Ratio (532/635)\</value>
257 </parameter>
258 <parameter>
259 <name>propertyMapping.ch1PercSd1</name>
260 <label>Percent pixels within 1 standard deviation</label>
261 <description />
262 <class>java.lang.String</class>
263 <value>\% &gt; B532+1SD\</value>
264 </parameter>
265 <parameter>
266 <name>rawDataType</name>
267 <label>Raw data type</label>
268 <description />
269 <class>java.lang.String</class>
270 <value>genepix</value>
271 </parameter>
272 <parameter>
273 <name>propertyMapping.ch2PercSd2</name>
274 <label>Percent pixels within 2 standard deviations</label>
275 <description />
276 <class>java.lang.String</class>
277 <value>\% &gt; B635+2SD\</value>
278 </parameter>
279 <parameter>
280 <name>blockColumnMapping</name>
281 <label>Block</label>
282 <description />
283 <class>java.lang.String</class>
284 <value>\Block\</value>
285 </parameter>
286 </configuration>
287</configfile>