DocBookSupport: reporter_importer_affymetrix2.xml

File reporter_importer_affymetrix2.xml, 8.7 KB (added by Jari Häkkinen, 16 years ago)
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2
3<!--
4 Copyright (C) 2007 Jari Hakkinen
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.
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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.
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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
23<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
24 <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
25 <configname>Affymetrix probe set importer 2</configname>
26 <description>Works for HG-U133A</description>
27 <parameter>
28 <name>maxDataColumns</name>
29 <label>Max data columns</label>
30 <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
31 <class />
32 <value />
33 </parameter>
34 <parameter>
35 <name>extendedColumnMapping.locusLink</name>
36 <label>LocusLink</label>
37 <description />
38 <class />
39 <value />
40 </parameter>
41 <parameter>
42 <name>trimQuotes</name>
43 <label>Remove quotes</label>
44 <description>If true quotes (" or ') around data value will be removed.</description>
45 <class>java.lang.Boolean</class>
46 <value>true</value>
47 </parameter>
48 <parameter>
49 <name>charset</name>
50 <label>Character set</label>
51 <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
52 <class>java.lang.String</class>
53 <value>ISO-8859-1</value>
54 </parameter>
55 <parameter>
56 <name>scoreColumnMapping</name>
57 <label>Score</label>
58 <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
59 <class />
60 <value />
61 </parameter>
62 <parameter>
63 <name>nameColumnMapping</name>
64 <label>Name</label>
65 <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
66 <class>java.lang.String</class>
67 <value>\Probe Set ID\</value>
68 </parameter>
69 <parameter>
70 <name>extendedColumnMapping.markers</name>
71 <label>Markers</label>
72 <description />
73 <class />
74 <value />
75 </parameter>
76 <parameter>
77 <name>extendedColumnMapping.vector</name>
78 <label>Vector</label>
79 <description>The vector from which the reporter is derived</description>
80 <class />
81 <value />
82 </parameter>
83 <parameter>
84 <name>extendedColumnMapping.nid</name>
85 <label>NID</label>
86 <description />
87 <class />
88 <value />
89 </parameter>
90 <parameter>
91 <name>descriptionColumnMapping</name>
92 <label>Description</label>
93 <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
94 <class />
95 <value />
96 </parameter>
97 <parameter>
98 <name>headerRegexp</name>
99 <label>Header</label>
100 <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
101 <class />
102 <value />
103 </parameter>
104 <parameter>
105 <name>reporterIdColumnMapping</name>
106 <label>Reporter ID</label>
107 <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
108 <class>java.lang.String</class>
109 <value>\Probe Set ID\</value>
110 </parameter>
111 <parameter>
112 <name>symbolColumnMapping</name>
113 <label>Gene symbol</label>
114 <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
115 <class>java.lang.String</class>
116 <value>\Gene Symbol\</value>
117 </parameter>
118 <parameter>
119 <name>extendedColumnMapping.antibiotics</name>
120 <label>Antibiotics</label>
121 <description />
122 <class />
123 <value />
124 </parameter>
125 <parameter>
126 <name>extendedColumnMapping.omim</name>
127 <label>OMIM</label>
128 <description />
129 <class />
130 <value />
131 </parameter>
132 <parameter>
133 <name>extendedColumnMapping.chromosome</name>
134 <label>Chromosome</label>
135 <description>The chromosome from which the reporter is derived</description>
136 <class />
137 <value />
138 </parameter>
139 <parameter>
140 <name>reporterType</name>
141 <label>Reporter type</label>
142 <description>The reporter type assigned to the imported reporters</description>
143 <class />
144 <value />
145 </parameter>
146 <parameter>
147 <name>dataHeaderRegexp</name>
148 <label>Data header</label>
149 <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
150 <class>java.lang.String</class>
151 <value>"Probe Set ID"\t"GeneChip Array"\t.*</value>
152 </parameter>
153 <parameter>
154 <name>dataSplitterRegexp</name>
155 <label>Data splitter</label>
156 <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
157 <class>java.lang.String</class>
158 <value>\t</value>
159 </parameter>
160 <parameter>
161 <name>extendedColumnMapping.length</name>
162 <label>Length</label>
163 <description>The length of the sequence</description>
164 <class />
165 <value />
166 </parameter>
167 <parameter>
168 <name>extendedColumnMapping.tissue</name>
169 <label>Tissue</label>
170 <description>The tissue from which the reporter is derived</description>
171 <class />
172 <value />
173 </parameter>
174 <parameter>
175 <name>extendedColumnMapping.accession</name>
176 <label>Accession</label>
177 <description />
178 <class />
179 <value />
180 </parameter>
181 <parameter>
182 <name>minDataColumns</name>
183 <label>Min data columns</label>
184 <description>The minimum number of columns for a line to be counted as a data line.</description>
185 <class />
186 <value />
187 </parameter>
188 <parameter>
189 <name>ignoreRegexp</name>
190 <label>Ignore</label>
191 <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
192 <class />
193 <value />
194 </parameter>
195 <parameter>
196 <name>reporterTypeColumnMapping</name>
197 <label>Reporter type</label>
198 <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
199 <class />
200 <value />
201 </parameter>
202 <parameter>
203 <name>extendedColumnMapping.library</name>
204 <label>Library</label>
205 <description>The library from which the reporter is derived</description>
206 <class />
207 <value />
208 </parameter>
209 <parameter>
210 <name>extendedColumnMapping.clusterId</name>
211 <label>Cluster ID</label>
212 <description>A unique identifier for a Unigene entry</description>
213 <class>java.lang.String</class>
214 <value>\UniGene ID\</value>
215 </parameter>
216 <parameter>
217 <name>decimalSeparator</name>
218 <label>Decimal separator</label>
219 <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
220 <class>java.lang.String</class>
221 <value>dot</value>
222 </parameter>
223 <parameter>
224 <name>dataFooterRegexp</name>
225 <label>Data footer</label>
226 <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
227 <class />
228 <value />
229 </parameter>
230 <parameter>
231 <name>extendedColumnMapping.cytoband</name>
232 <label>Cytoband</label>
233 <description>The cytoband from which the reporter is derived</description>
234 <class />
235 <value />
236 </parameter>
237 <parameter>
238 <name>extendedColumnMapping.sequence</name>
239 <label>Sequence</label>
240 <description>The nucleotide sequence of the reporter</description>
241 <class />
242 <value />
243 </parameter>
244 <parameter>
245 <name>extendedColumnMapping.species</name>
246 <label>Species</label>
247 <description>The organism from which the reporter is derived</description>
248 <class />
249 <value />
250 </parameter>
251 </configuration>
252</configfile>