1 | <?xml version="1.0" encoding="UTF-8"?> |
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2 | <!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile> |
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3 | <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxReporterImporter"> |
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4 | <configname>Illumina default reporter import</configname> |
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5 | <description>A standard configuration that assumes that the default configuration for extended properties are used + the extra extended properties that are shipped with this plug-in package</description> |
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6 | <parameter> |
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7 | <name>extendedColumnMapping.accession</name> |
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8 | <label>Accession</label> |
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9 | <description /> |
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10 | <class>java.lang.String</class> |
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11 | <value>\Accession\</value> |
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12 | </parameter> |
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13 | <parameter> |
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14 | <name>minDataColumns</name> |
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15 | <label>Min data columns</label> |
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16 | <description>The minimum number of columns for a line to be counted as a data line.</description> |
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17 | <class /> |
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18 | <value /> |
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19 | </parameter> |
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20 | <parameter> |
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21 | <name>extendedColumnMapping.cytoband</name> |
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22 | <label>Cytoband</label> |
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23 | <description>The cytoband from which the reporter is derived</description> |
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24 | <class /> |
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25 | <value /> |
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26 | </parameter> |
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27 | <parameter> |
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28 | <name>dataFooterRegexp</name> |
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29 | <label>Data footer</label> |
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30 | <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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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.source</name> |
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36 | <label>Source</label> |
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37 | <description /> |
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38 | <class>java.lang.String</class> |
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39 | <value>\Source\</value> |
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40 | </parameter> |
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41 | <parameter> |
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42 | <name>extendedColumnMapping.markers</name> |
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43 | <label>Markers</label> |
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44 | <description /> |
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45 | <class /> |
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46 | <value /> |
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47 | </parameter> |
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48 | <parameter> |
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49 | <name>extendedColumnMapping.omim</name> |
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50 | <label>OMIM</label> |
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51 | <description /> |
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52 | <class /> |
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53 | <value /> |
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54 | </parameter> |
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55 | <parameter> |
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56 | <name>extendedColumnMapping.searchKey</name> |
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57 | <label>Search key</label> |
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58 | <description /> |
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59 | <class>java.lang.String</class> |
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60 | <value>\Search_Key\</value> |
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61 | </parameter> |
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62 | <parameter> |
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63 | <name>extendedColumnMapping.tissue</name> |
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64 | <label>Tissue</label> |
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65 | <description>The tissue from which the reporter is derived</description> |
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66 | <class /> |
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67 | <value /> |
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68 | </parameter> |
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69 | <parameter> |
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70 | <name>descriptionColumnMapping</name> |
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71 | <label>Description</label> |
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72 | <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description> |
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73 | <class>java.lang.String</class> |
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74 | <value>\Definition\</value> |
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75 | </parameter> |
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76 | <parameter> |
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77 | <name>ignoreRegexp</name> |
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78 | <label>Ignore</label> |
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79 | <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</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.clusterId</name> |
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85 | <label>Cluster ID</label> |
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86 | <description>A unique identifier for a Unigene entry</description> |
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87 | <class>java.lang.String</class> |
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88 | <value>\Unigene_ID\</value> |
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89 | </parameter> |
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90 | <parameter> |
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91 | <name>decimalSeparator</name> |
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92 | <label>Decimal separator</label> |
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93 | <description>The decimal separator used in numeric values, if not specified dot is assumed.</description> |
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94 | <class>java.lang.String</class> |
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95 | <value>dot</value> |
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96 | </parameter> |
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97 | <parameter> |
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98 | <name>trimQuotes</name> |
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99 | <label>Remove quotes</label> |
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100 | <description>If true quotes (" or ') around data value will be removed.</description> |
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101 | <class>java.lang.Boolean</class> |
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102 | <value>true</value> |
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103 | </parameter> |
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104 | <parameter> |
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105 | <name>extendedColumnMapping.locusLink</name> |
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106 | <label>LocusLink</label> |
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107 | <description /> |
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108 | <class>java.lang.String</class> |
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109 | <value>\Entrez_Gene_ID\</value> |
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110 | </parameter> |
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111 | <parameter> |
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112 | <name>extendedColumnMapping.synonyms</name> |
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113 | <label>Synonyms</label> |
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114 | <description /> |
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115 | <class>java.lang.String</class> |
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116 | <value>\Synonyms\</value> |
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117 | </parameter> |
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118 | <parameter> |
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119 | <name>extendedColumnMapping.isoformType</name> |
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120 | <label>Isoform type</label> |
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121 | <description /> |
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122 | <class>java.lang.String</class> |
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123 | <value>\Probe_Type\</value> |
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124 | </parameter> |
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125 | <parameter> |
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126 | <name>extendedColumnMapping.sourceReferenceId</name> |
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127 | <label>Source reference id</label> |
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128 | <description /> |
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129 | <class>java.lang.String</class> |
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130 | <value>\Source_Reference_ID\</value> |
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131 | </parameter> |
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132 | <parameter> |
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133 | <name>extendedColumnMapping.ilmnGene</name> |
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134 | <label>ILMN Gene</label> |
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135 | <description /> |
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136 | <class>java.lang.String</class> |
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137 | <value>\ILMN_Gene\</value> |
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138 | </parameter> |
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139 | <parameter> |
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140 | <name>extendedColumnMapping.library</name> |
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141 | <label>Library</label> |
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142 | <description>The library from which the reporter is derived</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>maxDataColumns</name> |
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148 | <label>Max data columns</label> |
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149 | <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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150 | <class /> |
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151 | <value /> |
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152 | </parameter> |
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153 | <parameter> |
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154 | <name>extendedColumnMapping.probeCoordinates</name> |
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155 | <label>Probe coordinates</label> |
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156 | <description /> |
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157 | <class>java.lang.String</class> |
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158 | <value>\Probe_Coordinates\</value> |
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159 | </parameter> |
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160 | <parameter> |
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161 | <name>extendedColumnMapping.chromosome</name> |
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162 | <label>Chromosome</label> |
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163 | <description>The chromosome from which the reporter is derived</description> |
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164 | <class>java.lang.String</class> |
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165 | <value>\Chromosome\</value> |
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166 | </parameter> |
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167 | <parameter> |
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168 | <name>symbolColumnMapping</name> |
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169 | <label>Gene symbol</label> |
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170 | <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description> |
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171 | <class>java.lang.String</class> |
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172 | <value>\Symbol\</value> |
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173 | </parameter> |
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174 | <parameter> |
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175 | <name>headerRegexp</name> |
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176 | <label>Header</label> |
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177 | <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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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>scoreColumnMapping</name> |
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183 | <label>Score</label> |
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184 | <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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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>dataHeaderRegexp</name> |
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190 | <label>Data header</label> |
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191 | <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> |
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192 | <class>java.lang.String</class> |
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193 | <value>.*Probe_Id.+Array_Address_Id.*</value> |
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194 | </parameter> |
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195 | <parameter> |
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196 | <name>extendedColumnMapping.controlCompositeMap</name> |
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197 | <label>Control composite map</label> |
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198 | <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>reporterType</name> |
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204 | <label>Reporter type</label> |
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205 | <description>The reporter type assigned to the imported reporters</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.length</name> |
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211 | <label>Length</label> |
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212 | <description>The length of the sequence</description> |
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213 | <class /> |
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214 | <value /> |
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215 | </parameter> |
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216 | <parameter> |
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217 | <name>extendedColumnMapping.probeChrOrientation</name> |
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218 | <label>Probe chr orientation</label> |
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219 | <description /> |
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220 | <class>java.lang.String</class> |
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221 | <value>\Probe_Chr_Orientation\</value> |
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222 | </parameter> |
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223 | <parameter> |
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224 | <name>complexExpressions</name> |
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225 | <label>Complex column mappings</label> |
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226 | <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\' |
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227 | allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> |
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228 | <class>java.lang.String</class> |
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229 | <value>disallow</value> |
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230 | </parameter> |
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231 | <parameter> |
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232 | <name>reporterTypeColumnMapping</name> |
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233 | <label>Reporter type</label> |
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234 | <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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235 | <class /> |
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236 | <value /> |
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237 | </parameter> |
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238 | <parameter> |
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239 | <name>charset</name> |
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240 | <label>Character set</label> |
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241 | <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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242 | <class>java.lang.String</class> |
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243 | <value>ISO-8859-1</value> |
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244 | </parameter> |
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245 | <parameter> |
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246 | <name>extendedColumnMapping.controlGroupName</name> |
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247 | <label>Control group name</label> |
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248 | <description /> |
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249 | <class /> |
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250 | <value /> |
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251 | </parameter> |
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252 | <parameter> |
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253 | <name>extendedColumnMapping.controlGroupId</name> |
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254 | <label>Control group id</label> |
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255 | <description /> |
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256 | <class /> |
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257 | <value /> |
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258 | </parameter> |
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259 | <parameter> |
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260 | <name>dataSplitterRegexp</name> |
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261 | <label>Data splitter</label> |
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262 | <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description> |
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263 | <class>java.lang.String</class> |
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264 | <value>\t</value> |
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265 | </parameter> |
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266 | <parameter> |
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267 | <name>extendedColumnMapping.antibiotics</name> |
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268 | <label>Antibiotics</label> |
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269 | <description /> |
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270 | <class /> |
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271 | <value /> |
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272 | </parameter> |
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273 | <parameter> |
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274 | <name>reporterIdColumnMapping</name> |
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275 | <label>Reporter ID</label> |
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276 | <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description> |
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277 | <class>java.lang.String</class> |
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278 | <value>\Probe_Id\</value> |
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279 | </parameter> |
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280 | <parameter> |
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281 | <name>extendedColumnMapping.species</name> |
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282 | <label>Species</label> |
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283 | <description>The organism from which the reporter is derived</description> |
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284 | <class>java.lang.String</class> |
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285 | <value>\Species\</value> |
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286 | </parameter> |
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287 | <parameter> |
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288 | <name>extendedColumnMapping.sequence</name> |
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289 | <label>Sequence</label> |
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290 | <description>The nucleotide sequence of the reporter</description> |
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291 | <class>java.lang.String</class> |
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292 | <value>\Probe_Sequence\</value> |
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293 | </parameter> |
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294 | <parameter> |
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295 | <name>nameColumnMapping</name> |
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296 | <label>Name</label> |
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297 | <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description> |
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298 | <class>java.lang.String</class> |
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299 | <value>\Probe_Id\</value> |
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300 | </parameter> |
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301 | <parameter> |
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302 | <name>extendedColumnMapping.vector</name> |
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303 | <label>Vector</label> |
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304 | <description>The vector from which the reporter is derived</description> |
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305 | <class /> |
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306 | <value /> |
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307 | </parameter> |
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308 | <parameter> |
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309 | <name>extendedColumnMapping.nid</name> |
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310 | <label>NID</label> |
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311 | <description /> |
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312 | <class /> |
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313 | <value /> |
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314 | </parameter> |
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315 | </configuration> |
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316 | <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxFeatureImporter"> |
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317 | <configname>Features from BGX file</configname> |
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318 | <description>This is a standard configuration to import features from a BGX file.</description> |
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319 | <parameter> |
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320 | <name>trimQuotes</name> |
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321 | <label>Remove quotes</label> |
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322 | <description>If true quotes (" or ') around data value will be removed.</description> |
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323 | <class>java.lang.Boolean</class> |
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324 | <value>true</value> |
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325 | </parameter> |
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326 | <parameter> |
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327 | <name>dataHeaderRegexp</name> |
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328 | <label>Data header</label> |
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329 | <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> |
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330 | <class>java.lang.String</class> |
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331 | <value>.*Probe_Id.+Array_Address_Id.*</value> |
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332 | </parameter> |
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333 | <parameter> |
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334 | <name>reporterIdColumnMapping</name> |
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335 | <label>Reporter ID</label> |
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336 | <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description> |
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337 | <class>java.lang.String</class> |
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338 | <value>\Probe_Id\</value> |
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339 | </parameter> |
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340 | <parameter> |
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341 | <name>featureIdentification</name> |
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342 | <label>Identify features by</label> |
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343 | <description>Choose which method to use for identifying features: |
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344 | COORDINATES: Use block, meta-grid, row and column coordinates |
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345 | POSITION: Use a position number only |
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346 | FEATURE_ID: Use the feature ID value (string) |
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347 | In all cases, the identifier value must be unique.</description> |
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348 | <class>java.lang.String</class> |
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349 | <value>FEATURE_ID</value> |
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350 | </parameter> |
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351 | <parameter> |
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352 | <name>complexExpressions</name> |
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353 | <label>Complex column mappings</label> |
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354 | <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\' |
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355 | allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> |
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356 | <class>java.lang.String</class> |
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357 | <value>disallow</value> |
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358 | </parameter> |
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359 | <parameter> |
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360 | <name>charset</name> |
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361 | <label>Character set</label> |
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362 | <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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363 | <class>java.lang.String</class> |
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364 | <value>ISO-8859-1</value> |
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365 | </parameter> |
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366 | <parameter> |
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367 | <name>featureIdColumnMapping</name> |
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368 | <label>Feature ID</label> |
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369 | <description>Mapping that picks the feature's ID from the data columns. This column is only used when the array design uses the FEATURE_ID method for identifying features. In the other cases, the value is just stored as it is.For example: \Feature ID\</description> |
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370 | <class>java.lang.String</class> |
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371 | <value>\Array_Address_Id\</value> |
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372 | </parameter> |
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373 | <parameter> |
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374 | <name>dataSplitterRegexp</name> |
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375 | <label>Data splitter</label> |
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376 | <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description> |
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377 | <class>java.lang.String</class> |
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378 | <value>\t</value> |
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379 | </parameter> |
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380 | <parameter> |
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381 | <name>headerRegexp</name> |
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382 | <label>Header</label> |
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383 | <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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384 | <class>java.lang.String</class> |
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385 | <value>(.+)=(.*)</value> |
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386 | </parameter> |
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387 | </configuration> |
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388 | <configuration pluginClassName="net.sf.basedb.illumina.plugins.SnpReporterImporter"> |
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389 | <configname>Reporters from Illumina SNP manifest file</configname> |
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390 | <description>Import reporter annotations from an Illumina SNP manifest file.</description> |
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391 | <parameter> |
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392 | <name>extendedColumnMapping.accession</name> |
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393 | <label>Accession</label> |
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394 | <description /> |
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395 | <class /> |
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396 | <value /> |
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397 | </parameter> |
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398 | <parameter> |
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399 | <name>minDataColumns</name> |
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400 | <label>Min data columns</label> |
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401 | <description>The minimum number of columns for a line to be counted as a data line.</description> |
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402 | <class /> |
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403 | <value /> |
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404 | </parameter> |
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405 | <parameter> |
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406 | <name>dataFooterRegexp</name> |
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407 | <label>Data footer</label> |
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408 | <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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409 | <class /> |
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410 | <value /> |
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411 | </parameter> |
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412 | <parameter> |
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413 | <name>extendedColumnMapping.cytoband</name> |
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414 | <label>Cytoband</label> |
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415 | <description>The cytoband from which the reporter is derived</description> |
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416 | <class /> |
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417 | <value /> |
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418 | </parameter> |
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419 | <parameter> |
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420 | <name>extendedColumnMapping.markers</name> |
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421 | <label>Markers</label> |
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422 | <description /> |
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423 | <class /> |
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424 | <value /> |
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425 | </parameter> |
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426 | <parameter> |
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427 | <name>extendedColumnMapping.source</name> |
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428 | <label>Source</label> |
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429 | <description /> |
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430 | <class /> |
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431 | <value /> |
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432 | </parameter> |
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433 | <parameter> |
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434 | <name>extendedColumnMapping.omim</name> |
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435 | <label>OMIM</label> |
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436 | <description /> |
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437 | <class /> |
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438 | <value /> |
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439 | </parameter> |
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440 | <parameter> |
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441 | <name>extendedColumnMapping.searchKey</name> |
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442 | <label>Search key</label> |
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443 | <description /> |
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444 | <class /> |
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445 | <value /> |
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446 | </parameter> |
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447 | <parameter> |
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448 | <name>extendedColumnMapping.tissue</name> |
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449 | <label>Tissue</label> |
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450 | <description>The tissue from which the reporter is derived</description> |
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451 | <class /> |
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452 | <value /> |
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453 | </parameter> |
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454 | <parameter> |
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455 | <name>descriptionColumnMapping</name> |
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456 | <label>Description</label> |
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457 | <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description> |
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458 | <class /> |
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459 | <value /> |
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460 | </parameter> |
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461 | <parameter> |
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462 | <name>ignoreRegexp</name> |
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463 | <label>Ignore</label> |
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464 | <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description> |
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465 | <class /> |
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466 | <value /> |
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467 | </parameter> |
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468 | <parameter> |
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469 | <name>extendedColumnMapping.clusterId</name> |
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470 | <label>Cluster ID</label> |
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471 | <description>A unique identifier for a Unigene entry</description> |
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472 | <class /> |
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473 | <value /> |
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474 | </parameter> |
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475 | <parameter> |
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476 | <name>decimalSeparator</name> |
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477 | <label>Decimal separator</label> |
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478 | <description>The decimal separator used in numeric values, if not specified dot is assumed.</description> |
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479 | <class>java.lang.String</class> |
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480 | <value>dot</value> |
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481 | </parameter> |
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482 | <parameter> |
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483 | <name>extendedColumnMapping.ilmnStrand</name> |
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484 | <label>Ilmn strand</label> |
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485 | <description>Strand definition of the SNP</description> |
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486 | <class>java.lang.String</class> |
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487 | <value>\IlmnStrand\</value> |
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488 | </parameter> |
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489 | <parameter> |
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490 | <name>extendedColumnMapping.snp</name> |
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491 | <label>SNP</label> |
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492 | <description>Type of SNP</description> |
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493 | <class>java.lang.String</class> |
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494 | <value>\SNP\</value> |
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495 | </parameter> |
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496 | <parameter> |
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497 | <name>extendedColumnMapping.startPosition</name> |
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498 | <label>Start position</label> |
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499 | <description>Start position</description> |
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500 | <class>java.lang.String</class> |
---|
501 | <value>\MapInfo\</value> |
---|
502 | </parameter> |
---|
503 | <parameter> |
---|
504 | <name>trimQuotes</name> |
---|
505 | <label>Remove quotes</label> |
---|
506 | <description>If true quotes (" or ') around data value will be removed.</description> |
---|
507 | <class>java.lang.Boolean</class> |
---|
508 | <value>true</value> |
---|
509 | </parameter> |
---|
510 | <parameter> |
---|
511 | <name>extendedColumnMapping.locusLink</name> |
---|
512 | <label>LocusLink</label> |
---|
513 | <description /> |
---|
514 | <class /> |
---|
515 | <value /> |
---|
516 | </parameter> |
---|
517 | <parameter> |
---|
518 | <name>extendedColumnMapping.synonyms</name> |
---|
519 | <label>Synonyms</label> |
---|
520 | <description /> |
---|
521 | <class /> |
---|
522 | <value /> |
---|
523 | </parameter> |
---|
524 | <parameter> |
---|
525 | <name>extendedColumnMapping.isoformType</name> |
---|
526 | <label>Isoform type</label> |
---|
527 | <description /> |
---|
528 | <class /> |
---|
529 | <value /> |
---|
530 | </parameter> |
---|
531 | <parameter> |
---|
532 | <name>extendedColumnMapping.sourceReferenceId</name> |
---|
533 | <label>Source reference id</label> |
---|
534 | <description /> |
---|
535 | <class /> |
---|
536 | <value /> |
---|
537 | </parameter> |
---|
538 | <parameter> |
---|
539 | <name>extendedColumnMapping.ilmnGene</name> |
---|
540 | <label>ILMN Gene</label> |
---|
541 | <description /> |
---|
542 | <class /> |
---|
543 | <value /> |
---|
544 | </parameter> |
---|
545 | <parameter> |
---|
546 | <name>extendedColumnMapping.library</name> |
---|
547 | <label>Library</label> |
---|
548 | <description>The library from which the reporter is derived</description> |
---|
549 | <class /> |
---|
550 | <value /> |
---|
551 | </parameter> |
---|
552 | <parameter> |
---|
553 | <name>maxDataColumns</name> |
---|
554 | <label>Max data columns</label> |
---|
555 | <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> |
---|
556 | <class /> |
---|
557 | <value /> |
---|
558 | </parameter> |
---|
559 | <parameter> |
---|
560 | <name>extendedColumnMapping.chromosome</name> |
---|
561 | <label>Chromosome</label> |
---|
562 | <description>The chromosome from which the reporter is derived</description> |
---|
563 | <class>java.lang.String</class> |
---|
564 | <value>\Chr\</value> |
---|
565 | </parameter> |
---|
566 | <parameter> |
---|
567 | <name>symbolColumnMapping</name> |
---|
568 | <label>Gene symbol</label> |
---|
569 | <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description> |
---|
570 | <class /> |
---|
571 | <value /> |
---|
572 | </parameter> |
---|
573 | <parameter> |
---|
574 | <name>headerRegexp</name> |
---|
575 | <label>Header</label> |
---|
576 | <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description> |
---|
577 | <class /> |
---|
578 | <value /> |
---|
579 | </parameter> |
---|
580 | <parameter> |
---|
581 | <name>scoreColumnMapping</name> |
---|
582 | <label>Score</label> |
---|
583 | <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description> |
---|
584 | <class /> |
---|
585 | <value /> |
---|
586 | </parameter> |
---|
587 | <parameter> |
---|
588 | <name>dataHeaderRegexp</name> |
---|
589 | <label>Data header</label> |
---|
590 | <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> |
---|
591 | <class>java.lang.String</class> |
---|
592 | <value>IlmnID,.*AddressA_ID.*</value> |
---|
593 | </parameter> |
---|
594 | <parameter> |
---|
595 | <name>extendedColumnMapping.controlCompositeMap</name> |
---|
596 | <label>Control composite map</label> |
---|
597 | <description /> |
---|
598 | <class /> |
---|
599 | <value /> |
---|
600 | </parameter> |
---|
601 | <parameter> |
---|
602 | <name>reporterType</name> |
---|
603 | <label>Reporter type</label> |
---|
604 | <description>The reporter type assigned to the imported reporters</description> |
---|
605 | <class /> |
---|
606 | <value /> |
---|
607 | </parameter> |
---|
608 | <parameter> |
---|
609 | <name>extendedColumnMapping.length</name> |
---|
610 | <label>Length</label> |
---|
611 | <description>The length of the sequence</description> |
---|
612 | <class /> |
---|
613 | <value /> |
---|
614 | </parameter> |
---|
615 | <parameter> |
---|
616 | <name>extendedColumnMapping.probeChrOrientation</name> |
---|
617 | <label>Probe chr orientation</label> |
---|
618 | <description /> |
---|
619 | <class /> |
---|
620 | <value /> |
---|
621 | </parameter> |
---|
622 | <parameter> |
---|
623 | <name>reporterTypeColumnMapping</name> |
---|
624 | <label>Reporter type</label> |
---|
625 | <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description> |
---|
626 | <class /> |
---|
627 | <value /> |
---|
628 | </parameter> |
---|
629 | <parameter> |
---|
630 | <name>complexExpressions</name> |
---|
631 | <label>Complex column mappings</label> |
---|
632 | <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\' |
---|
633 | allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> |
---|
634 | <class>java.lang.String</class> |
---|
635 | <value>disallow</value> |
---|
636 | </parameter> |
---|
637 | <parameter> |
---|
638 | <name>extendedColumnMapping.controlGroupName</name> |
---|
639 | <label>Control group name</label> |
---|
640 | <description /> |
---|
641 | <class /> |
---|
642 | <value /> |
---|
643 | </parameter> |
---|
644 | <parameter> |
---|
645 | <name>charset</name> |
---|
646 | <label>Character set</label> |
---|
647 | <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description> |
---|
648 | <class>java.lang.String</class> |
---|
649 | <value>ISO-8859-1</value> |
---|
650 | </parameter> |
---|
651 | <parameter> |
---|
652 | <name>extendedColumnMapping.probeCoordinates</name> |
---|
653 | <label>Probe coordinates</label> |
---|
654 | <description /> |
---|
655 | <class /> |
---|
656 | <value /> |
---|
657 | </parameter> |
---|
658 | <parameter> |
---|
659 | <name>extendedColumnMapping.controlGroupId</name> |
---|
660 | <label>Control group id</label> |
---|
661 | <description /> |
---|
662 | <class /> |
---|
663 | <value /> |
---|
664 | </parameter> |
---|
665 | <parameter> |
---|
666 | <name>dataSplitterRegexp</name> |
---|
667 | <label>Data splitter</label> |
---|
668 | <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description> |
---|
669 | <class>java.lang.String</class> |
---|
670 | <value>,</value> |
---|
671 | </parameter> |
---|
672 | <parameter> |
---|
673 | <name>extendedColumnMapping.antibiotics</name> |
---|
674 | <label>Antibiotics</label> |
---|
675 | <description /> |
---|
676 | <class /> |
---|
677 | <value /> |
---|
678 | </parameter> |
---|
679 | <parameter> |
---|
680 | <name>reporterIdColumnMapping</name> |
---|
681 | <label>Reporter ID</label> |
---|
682 | <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description> |
---|
683 | <class>java.lang.String</class> |
---|
684 | <value>\IlmnID\</value> |
---|
685 | </parameter> |
---|
686 | <parameter> |
---|
687 | <name>extendedColumnMapping.species</name> |
---|
688 | <label>Species</label> |
---|
689 | <description>The organism from which the reporter is derived</description> |
---|
690 | <class>java.lang.String</class> |
---|
691 | <value>\Species\</value> |
---|
692 | </parameter> |
---|
693 | <parameter> |
---|
694 | <name>extendedColumnMapping.sequence</name> |
---|
695 | <label>Sequence</label> |
---|
696 | <description>The nucleotide sequence of the reporter</description> |
---|
697 | <class /> |
---|
698 | <value /> |
---|
699 | </parameter> |
---|
700 | <parameter> |
---|
701 | <name>nameColumnMapping</name> |
---|
702 | <label>Name</label> |
---|
703 | <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description> |
---|
704 | <class>java.lang.String</class> |
---|
705 | <value>\Name\</value> |
---|
706 | </parameter> |
---|
707 | <parameter> |
---|
708 | <name>extendedColumnMapping.vector</name> |
---|
709 | <label>Vector</label> |
---|
710 | <description>The vector from which the reporter is derived</description> |
---|
711 | <class /> |
---|
712 | <value /> |
---|
713 | </parameter> |
---|
714 | <parameter> |
---|
715 | <name>extendedColumnMapping.nid</name> |
---|
716 | <label>NID</label> |
---|
717 | <description /> |
---|
718 | <class /> |
---|
719 | <value /> |
---|
720 | </parameter> |
---|
721 | </configuration> |
---|
722 | </configfile> |
---|