DocBookSupport: reporter_importer_affymetrix.xml

File reporter_importer_affymetrix.xml, 5.1 KB (added by Jari Häkkinen, 13 years ago)
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd">
3
4<!--
5  Copyright (C) 2007 Jari Hakkinen
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or modify it
11  under the terms of the GNU General Public License as published by
12  the Free Software Foundation; either version 3 of the License, or
13  (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful, but WITHOUT
16  ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
17  or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
18  License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23
24<configfile>
25  <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
26    <configname>Affymetrix probe set importer</configname>
27    <description />
28    <parameter>
29      <name>maxDataColumns</name>
30      <label>Max data columns</label>
31      <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>
32      <class />
33      <value />
34    </parameter>
35    <parameter>
36      <name>dataHeaderRegexp</name>
37      <label>Data header</label>
38      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
39      <class>java.lang.String</class>
40      <value>"Probe Set ID","GeneChip Array",.*</value>
41    </parameter>
42    <parameter>
43      <name>trimQuotes</name>
44      <label>Remove quotes</label>
45      <description>If true quotes (" or ') around data value will be removed.</description>
46      <class>java.lang.Boolean</class>
47      <value>true</value>
48    </parameter>
49    <parameter>
50      <name>dataSplitterRegexp</name>
51      <label>Data splitter</label>
52      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
53      <class>java.lang.String</class>
54      <value>(?!"),(?=")</value>
55    </parameter>
56    <parameter>
57      <name>scoreColumnMapping</name>
58      <label>Score</label>
59      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
60      <class />
61      <value />
62    </parameter>
63    <parameter>
64      <name>nameColumnMapping</name>
65      <label>Name</label>
66      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
67      <class>java.lang.String</class>
68      <value>\Probe Set ID\</value>
69    </parameter>
70    <parameter>
71      <name>minDataColumns</name>
72      <label>Min data columns</label>
73      <description>The minimum number of columns for a line to be counted as a data line.</description>
74      <class />
75      <value />
76    </parameter>
77    <parameter>
78      <name>ignoreRegexp</name>
79      <label>Ignore</label>
80      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
81      <class />
82      <value />
83    </parameter>
84    <parameter>
85      <name>descriptionColumnMapping</name>
86      <label>Description</label>
87      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
88      <class />
89      <value />
90    </parameter>
91    <parameter>
92      <name>dataFooterRegexp</name>
93      <label>Data footer</label>
94      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
95      <class />
96      <value />
97    </parameter>
98    <parameter>
99      <name>reporterIdColumnMapping</name>
100      <label>Reporter ID</label>
101      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
102      <class>java.lang.String</class>
103      <value>\Probe Set ID\</value>
104    </parameter>
105    <parameter>
106      <name>symbolColumnMapping</name>
107      <label>Gene symbol</label>
108      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
109      <class />
110      <value />
111    </parameter>
112    <parameter>
113      <name>headerRegexp</name>
114      <label>Header</label>
115      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
116      <class />
117      <value />
118    </parameter>
119    <parameter>
120      <name>extendedColumnMapping.unigeneId</name>
121      <label>UniGene ID</label>
122      <description>A unique identifier for a UniGene entry</description>
123      <class>java.lang.String</class>
124      <value>\UniGene ID\</value>
125    </parameter>
126    <parameter>
127      <name>reporterType</name>
128      <label>Reporter type</label>
129      <description>The reporter type assigned to the imported reporters</description>
130      <class />
131      <value />
132    </parameter>
133  </configuration>
134</configfile>