1 | <?xml version="1.0" encoding="UTF-8"?>
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2 |
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3 | <!--
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4 | Copyright (C) 2007 Jari Hakkinen
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5 |
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6 | This file is part of BASE - BioArray Software Environment.
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7 | Available at http://base.thep.lu.se/
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8 |
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9 | BASE is free software; you can redistribute it and/or modify it
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10 | under the terms of the GNU General Public License as published by
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11 | the Free Software Foundation; either version 3 of the License, or
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12 | (at your option) any later version.
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13 |
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14 | BASE is distributed in the hope that it will be useful, but WITHOUT
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15 | ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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16 | or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
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17 | License for more details.
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18 |
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19 | You should have received a copy of the GNU General Public License
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20 | along with BASE. If not, see <http://www.gnu.org/licenses/>.
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21 | -->
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22 |
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23 | <!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
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24 | <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
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25 | <configname>Affymetrix probe set importer 2</configname>
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26 | <description>Works for HG-U133A</description>
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27 | <parameter>
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28 | <name>maxDataColumns</name>
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29 | <label>Max data columns</label>
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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>
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31 | <class />
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32 | <value />
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33 | </parameter>
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34 | <parameter>
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35 | <name>extendedColumnMapping.locusLink</name>
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36 | <label>LocusLink</label>
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37 | <description />
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38 | <class />
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39 | <value />
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40 | </parameter>
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41 | <parameter>
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42 | <name>trimQuotes</name>
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43 | <label>Remove quotes</label>
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44 | <description>If true quotes (" or ') around data value will be removed.</description>
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45 | <class>java.lang.Boolean</class>
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46 | <value>true</value>
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47 | </parameter>
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48 | <parameter>
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49 | <name>charset</name>
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50 | <label>Character set</label>
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51 | <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
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52 | <class>java.lang.String</class>
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53 | <value>ISO-8859-1</value>
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54 | </parameter>
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55 | <parameter>
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56 | <name>scoreColumnMapping</name>
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57 | <label>Score</label>
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58 | <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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59 | <class />
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60 | <value />
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61 | </parameter>
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62 | <parameter>
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63 | <name>nameColumnMapping</name>
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64 | <label>Name</label>
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65 | <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
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66 | <class>java.lang.String</class>
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67 | <value>\Probe Set ID\</value>
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68 | </parameter>
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69 | <parameter>
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70 | <name>extendedColumnMapping.markers</name>
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71 | <label>Markers</label>
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72 | <description />
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73 | <class />
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74 | <value />
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75 | </parameter>
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76 | <parameter>
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77 | <name>extendedColumnMapping.vector</name>
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78 | <label>Vector</label>
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79 | <description>The vector from which the reporter is derived</description>
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80 | <class />
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81 | <value />
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82 | </parameter>
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83 | <parameter>
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84 | <name>extendedColumnMapping.nid</name>
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85 | <label>NID</label>
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86 | <description />
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87 | <class />
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88 | <value />
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89 | </parameter>
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90 | <parameter>
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91 | <name>descriptionColumnMapping</name>
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92 | <label>Description</label>
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93 | <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
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94 | <class />
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95 | <value />
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96 | </parameter>
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97 | <parameter>
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98 | <name>headerRegexp</name>
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99 | <label>Header</label>
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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>
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101 | <class />
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102 | <value />
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103 | </parameter>
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104 | <parameter>
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105 | <name>reporterIdColumnMapping</name>
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106 | <label>Reporter ID</label>
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107 | <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
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108 | <class>java.lang.String</class>
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109 | <value>\Probe Set ID\</value>
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110 | </parameter>
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111 | <parameter>
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112 | <name>symbolColumnMapping</name>
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113 | <label>Gene symbol</label>
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114 | <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
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115 | <class>java.lang.String</class>
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116 | <value>\Gene Symbol\</value>
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117 | </parameter>
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118 | <parameter>
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119 | <name>extendedColumnMapping.antibiotics</name>
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120 | <label>Antibiotics</label>
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121 | <description />
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122 | <class />
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123 | <value />
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124 | </parameter>
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125 | <parameter>
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126 | <name>extendedColumnMapping.omim</name>
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127 | <label>OMIM</label>
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128 | <description />
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129 | <class />
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130 | <value />
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131 | </parameter>
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132 | <parameter>
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133 | <name>extendedColumnMapping.chromosome</name>
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134 | <label>Chromosome</label>
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135 | <description>The chromosome from which the reporter is derived</description>
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136 | <class />
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137 | <value />
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138 | </parameter>
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139 | <parameter>
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140 | <name>reporterType</name>
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141 | <label>Reporter type</label>
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142 | <description>The reporter type assigned to the imported reporters</description>
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143 | <class />
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144 | <value />
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145 | </parameter>
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146 | <parameter>
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147 | <name>dataHeaderRegexp</name>
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148 | <label>Data header</label>
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149 | <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
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150 | <class>java.lang.String</class>
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151 | <value>"Probe Set ID"\t"GeneChip Array"\t.*</value>
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152 | </parameter>
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153 | <parameter>
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154 | <name>dataSplitterRegexp</name>
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155 | <label>Data splitter</label>
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156 | <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
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157 | <class>java.lang.String</class>
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158 | <value>\t</value>
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159 | </parameter>
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160 | <parameter>
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161 | <name>extendedColumnMapping.length</name>
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162 | <label>Length</label>
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163 | <description>The length of the sequence</description>
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164 | <class />
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165 | <value />
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166 | </parameter>
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167 | <parameter>
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168 | <name>extendedColumnMapping.tissue</name>
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169 | <label>Tissue</label>
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170 | <description>The tissue from which the reporter is derived</description>
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171 | <class />
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172 | <value />
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173 | </parameter>
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174 | <parameter>
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175 | <name>extendedColumnMapping.accession</name>
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176 | <label>Accession</label>
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177 | <description />
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178 | <class />
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179 | <value />
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180 | </parameter>
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181 | <parameter>
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182 | <name>minDataColumns</name>
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183 | <label>Min data columns</label>
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184 | <description>The minimum number of columns for a line to be counted as a data line.</description>
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185 | <class />
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186 | <value />
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187 | </parameter>
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188 | <parameter>
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189 | <name>ignoreRegexp</name>
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190 | <label>Ignore</label>
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191 | <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
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192 | <class />
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193 | <value />
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194 | </parameter>
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195 | <parameter>
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196 | <name>reporterTypeColumnMapping</name>
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197 | <label>Reporter type</label>
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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>
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199 | <class />
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200 | <value />
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201 | </parameter>
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202 | <parameter>
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203 | <name>extendedColumnMapping.library</name>
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204 | <label>Library</label>
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205 | <description>The library from which the reporter is derived</description>
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206 | <class />
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207 | <value />
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208 | </parameter>
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209 | <parameter>
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210 | <name>extendedColumnMapping.clusterId</name>
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211 | <label>Cluster ID</label>
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212 | <description>A unique identifier for a Unigene entry</description>
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213 | <class>java.lang.String</class>
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214 | <value>\UniGene ID\</value>
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215 | </parameter>
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216 | <parameter>
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217 | <name>decimalSeparator</name>
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218 | <label>Decimal separator</label>
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219 | <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
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220 | <class>java.lang.String</class>
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221 | <value>dot</value>
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222 | </parameter>
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223 | <parameter>
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224 | <name>dataFooterRegexp</name>
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225 | <label>Data footer</label>
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226 | <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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227 | <class />
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228 | <value />
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229 | </parameter>
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230 | <parameter>
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231 | <name>extendedColumnMapping.cytoband</name>
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232 | <label>Cytoband</label>
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233 | <description>The cytoband from which the reporter is derived</description>
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234 | <class />
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235 | <value />
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236 | </parameter>
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237 | <parameter>
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238 | <name>extendedColumnMapping.sequence</name>
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239 | <label>Sequence</label>
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240 | <description>The nucleotide sequence of the reporter</description>
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241 | <class />
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242 | <value />
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243 | </parameter>
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244 | <parameter>
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245 | <name>extendedColumnMapping.species</name>
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246 | <label>Species</label>
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247 | <description>The organism from which the reporter is derived</description>
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248 | <class />
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249 | <value />
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250 | </parameter>
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251 | </configuration>
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252 | </configfile>
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