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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