DocBookSupport: reporter_importer_affymetrix2.xml

File reporter_importer_affymetrix2.xml, 8.7 KB (added by Jari Häkkinen, 14 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.
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
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>