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