source: plugins/base2/net.sf.basedb.agilent/trunk/config/Agilent1chFull-plugin-configuration.xml @ 1199

Last change on this file since 1199 was 1199, checked in by Jari Häkkinen, 12 years ago

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
3  <configuration pluginClassName="net.sf.basedb.plugins.RawDataFlatFileImporter">
4    <configname>Agilent 1 channel raw data import (full format files)</configname>
5    <description>Configuration to import raw data from Agilent 'full' format files. Created using a result file from 1 channel assay on 4X44K GE.</description>
6    <parameter>
7      <name>propertyMapping.gNumSatPix</name>
8      <label>G saturated pixels</label>
9      <description>Total number of saturated pixels per feature, computed per channel.</description>
10      <class>java.lang.String</class>
11      <value>\gNumSatPix\</value>
12    </parameter>
13    <parameter>
14      <name>ignoreRegexp</name>
15      <label>Ignore</label>
16      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
17      <class />
18      <value />
19    </parameter>
20    <parameter>
21      <name>propertyMapping.gSpatialDetrendSurfaceValue</name>
22      <label>G surface value</label>
23      <description>Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet.</description>
24      <class>java.lang.String</class>
25      <value>\gSpatialDetrendSurfaceValue\</value>
26    </parameter>
27    <parameter>
28      <name>decimalSeparator</name>
29      <label>Decimal separator</label>
30      <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
31      <class>java.lang.String</class>
32      <value>dot</value>
33    </parameter>
34    <parameter>
35      <name>blockColumnMapping</name>
36      <label>Block</label>
37      <description>Mapping that picks the spot's block number from the data columns. This column is only used when the raw data is connected to an array design which uses the COORDINATES method for identifying features. In all other cases, the value is stored as is.For example: \Block\</description>
38      <class />
39      <value />
40    </parameter>
41    <parameter>
42      <name>propertyMapping.gIsFeatNonUnifOL</name>
43      <label>G non-uniform outlier</label>
44      <description>Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier.</description>
45      <class>java.lang.String</class>
46      <value>\gIsFeatNonUnifOL\</value>
47    </parameter>
48    <parameter>
49      <name>trimQuotes</name>
50      <label>Remove quotes</label>
51      <description>If true quotes (" or ') around data value will be removed.</description>
52      <class>java.lang.Boolean</class>
53      <value>true</value>
54    </parameter>
55    <parameter>
56      <name>propertyMapping.gIsWellAboveBG</name>
57      <label>G well above bg</label>
58      <description>Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG.</description>
59      <class>java.lang.String</class>
60      <value>\gIsWellAboveBG\</value>
61    </parameter>
62    <parameter>
63      <name>propertyMapping.gSurrogateUsed</name>
64      <label>G surrogate used</label>
65      <description>The green surrogate value used.</description>
66      <class>java.lang.String</class>
67      <value>\gSurrogateUsed\</value>
68    </parameter>
69    <parameter>
70      <name>dataHeaderRegexp</name>
71      <label>Data header</label>
72      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
73      <class>java.lang.String</class>
74      <value>FEATURES\tFeatureNum\tRow\tCol.*\tgSurrogateUsed.*\tgProcessedSignal\tgProcessedSigError.*</value>
75    </parameter>
76    <parameter>
77      <name>propertyMapping.gIsBGPopnOL</name>
78      <label>G bg population outlier</label>
79      <description>Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier.</description>
80      <class>java.lang.String</class>
81      <value>\gIsBGPopnOL\</value>
82    </parameter>
83    <parameter>
84      <name>positionColumnMapping</name>
85      <label>Position</label>
86      <description>Mapping that picks the spot's position from the data columns. This column is only used when the raw data is connected to an array design which uses the POSITION method for identifying features. If the raw data is not connected to an array design position values will automatically be generated if no mapping has been specified. In allcases, position value must be unique.Mapping example: \Position\</description>
87      <class />
88      <value />
89    </parameter>
90    <parameter>
91      <name>charset</name>
92      <label>Character set</label>
93      <description>The character set to use when reading the file. This setting overrides the character set specified by the file. If neither this parameter nor the file specifies a character set, the system default is used (ISO-8859-1).</description>
94      <class>java.lang.String</class>
95      <value>ISO-8859-1</value>
96    </parameter>
97    <parameter>
98      <name>featureIdColumnMapping</name>
99      <label>Feature ID</label>
100      <description>Mapping that picks the spot's feature ID from the data columns. This column is only used when the raw data is connected to an array design which uses the FEATURE_ID method for identifying features. The value is not saved to the database.For example: \Feature ID\</description>
101      <class>java.lang.String</class>
102      <value>\FeatureNum\</value>
103    </parameter>
104    <parameter>
105      <name>rawDataType</name>
106      <label>Raw data type</label>
107      <description>The type of raw data that this importer will import.</description>
108      <class>java.lang.String</class>
109      <value>agilent1ch</value>
110    </parameter>
111    <parameter>
112      <name>dataSplitterRegexp</name>
113      <label>Data splitter</label>
114      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
115      <class>java.lang.String</class>
116      <value>\t</value>
117    </parameter>
118    <parameter>
119      <name>propertyMapping.IsManualFlag</name>
120      <label>Manual flag</label>
121      <description>If a feature has been moved manually this flag will be set to 1.</description>
122      <class>java.lang.String</class>
123      <value>\IsManualFlag\</value>
124    </parameter>
125    <parameter>
126      <name>propertyMapping.gSpatialDetrendIsInFilteredSet</name>
127      <label>G spatial trend</label>
128      <description>Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features.</description>
129      <class>java.lang.String</class>
130      <value>\gSpatialDetrendIsInFilteredSet\</value>
131    </parameter>
132    <parameter>
133      <name>minDataColumns</name>
134      <label>Min data columns</label>
135      <description>The minimum number of columns for a line to be counted as a data line.</description>
136      <class />
137      <value />
138    </parameter>
139    <parameter>
140      <name>propertyMapping.ErrorModel</name>
141      <label>Error model</label>
142      <description>ErrorModel Indicates the error model that the user chose for feature extraction. A 0 indicates use of the Propogated Error Model. A 1 indicates use of the Universal Error Model.</description>
143      <class>java.lang.String</class>
144      <value>\ErrorModel\</value>
145    </parameter>
146    <parameter>
147      <name>dataFooterRegexp</name>
148      <label>Data footer</label>
149      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
150      <class />
151      <value />
152    </parameter>
153    <parameter>
154      <name>propertyMapping.gNumBGUsed</name>
155      <label>G background pixels</label>
156      <description>A count of the number of background pixels used in the green channel.</description>
157      <class>java.lang.String</class>
158      <value>\gBGNumPix\</value>
159    </parameter>
160    <parameter>
161      <name>propertyMapping.gBGPixSDev</name>
162      <label>G background pixel SDev</label>
163      <description>Standard deviation of  all inlier pixels per Local BG of each feature, computed independently in each channelStandard deviation of  all inlier pixels per Local BG of each feature, computed independently in each channel.</description>
164      <class>java.lang.String</class>
165      <value>\gBGPixSDev\</value>
166    </parameter>
167    <parameter>
168      <name>propertyMapping.gIsBGNonUnifOL</name>
169      <label>G bg non-uniform outlier</label>
170      <description>Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier.</description>
171      <class>java.lang.String</class>
172      <value>\gIsBGNonUnifOL\</value>
173    </parameter>
174    <parameter>
175      <name>yColumnMapping</name>
176      <label>Y</label>
177      <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
178      <class>java.lang.String</class>
179      <value>\PositionY\</value>
180    </parameter>
181    <parameter>
182      <name>propertyMapping.gBGNumPix</name>
183      <label>G background pixels</label>
184      <description>Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel.</description>
185      <class>java.lang.String</class>
186      <value>\gBGNumPix\</value>
187    </parameter>
188    <parameter>
189      <name>propertyMapping.gIsSaturated</name>
190      <label>G is saturated</label>
191      <description>Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated.</description>
192      <class>java.lang.String</class>
193      <value>\gIsSaturated\</value>
194    </parameter>
195    <parameter>
196      <name>propertyMapping.gMedianSignal</name>
197      <label>G median signal</label>
198      <description>Raw median signal of feature in green channel.</description>
199      <class>java.lang.String</class>
200      <value>\gMedianSignal\</value>
201    </parameter>
202    <parameter>
203      <name>metaGridXColumnMapping</name>
204      <label>MetaGridX</label>
205      <description>Mapping that picks the spot's meta-Grid X-axis from the data columns. This column is only used when the raw data is connected to an array design which uses the COORDINATES method for identifying features. In all other cases, the value is stored as is.For example: \Meta grid X\</description>
206      <class />
207      <value />
208    </parameter>
209    <parameter>
210      <name>propertyMapping.gPixSDev</name>
211      <label>G pixel SDev</label>
212      <description>Standard deviation of all inlier pixels per feature; this is computed independently in each channel.</description>
213      <class>java.lang.String</class>
214      <value>\gPixSDev\</value>
215    </parameter>
216    <parameter>
217      <name>maxDataColumns</name>
218      <label>Max data columns</label>
219      <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>
220      <class />
221      <value />
222    </parameter>
223    <parameter>
224      <name>propertyMapping.gBGUsed</name>
225      <label>G bg used</label>
226      <description>Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel.</description>
227      <class>java.lang.String</class>
228      <value>\gBGUsed\</value>
229    </parameter>
230    <parameter>
231      <name>propertyMapping.gIsFound</name>
232      <label>G is found</label>
233      <description>A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong.</description>
234      <class>java.lang.String</class>
235      <value>\gIsFound\</value>
236    </parameter>
237    <parameter>
238      <name>metaGridYColumnMapping</name>
239      <label>MetaGridY</label>
240      <description>Mapping that picks the spot's meta-Grid Y-axis from the data columns. This column is only used when the raw data is connected to an array design which uses the COORDINATES method for identifying features. In all other cases, the value is stored as is.For example: \Meta grid Y\</description>
241      <class />
242      <value />
243    </parameter>
244    <parameter>
245      <name>headerRegexp</name>
246      <label>Header</label>
247      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
248      <class />
249      <value />
250    </parameter>
251    <parameter>
252      <name>propertyMapping.gMeanSignal</name>
253      <label>G mean signal</label>
254      <description>Raw mean signal of feature in green channel.</description>
255      <class>java.lang.String</class>
256      <value>\gMeanSignal\</value>
257    </parameter>
258    <parameter>
259      <name>complexExpressions</name>
260      <label>Complex column mappings</label>
261      <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\'
262allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description>
263      <class>java.lang.String</class>
264      <value>disallow</value>
265    </parameter>
266    <parameter>
267      <name>propertyMapping.gProcessedSignal</name>
268      <label>G processed signal</label>
269      <description>The propagated feature signal, per channel, used for computation of log ratio.</description>
270      <class>java.lang.String</class>
271      <value>\gProcessedSignal\</value>
272    </parameter>
273    <parameter>
274      <name>columnColumnMapping</name>
275      <label>Column</label>
276      <description>Mapping that picks the spot's column coordinate from the data columns. This column is only used when the raw data is connected to an array design which uses the COORDINATES method for identifying features. In all other cases, the value is stored as is.For example: \Column\</description>
277      <class>java.lang.String</class>
278      <value>\Col\</value>
279    </parameter>
280    <parameter>
281      <name>propertyMapping.gIsPosAndSignif</name>
282      <label>G &gt; 0 and significant</label>
283      <description>Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background.</description>
284      <class>java.lang.String</class>
285      <value>\gIsPosAndSignif\</value>
286    </parameter>
287    <parameter>
288      <name>reporterIdColumnMapping</name>
289      <label>Reporter ID</label>
290      <description>Mapping that picks the 'External ID' of the spot's reporter from the data columns. For example: \ID\</description>
291      <class>java.lang.String</class>
292      <value>\ProbeName\</value>
293    </parameter>
294    <parameter>
295      <name>propertyMapping.gPValFeatEqBG</name>
296      <label>G p-value</label>
297      <description>P-value from t-test of significance between green Mean signal and green background.</description>
298      <class>java.lang.String</class>
299      <value>\gPValFeatEqBG\</value>
300    </parameter>
301    <parameter>
302      <name>propertyMapping.gNumPix</name>
303      <label>G pixels</label>
304      <description>Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels.</description>
305      <class>java.lang.String</class>
306      <value>\gNumPix\</value>
307    </parameter>
308    <parameter>
309      <name>propertyMapping.gBGMedianSignal</name>
310      <label>G median background</label>
311      <description>Median local background signal (local to corresponding feature) computed per channel.</description>
312      <class>java.lang.String</class>
313      <value>\gBGMedianSignal\</value>
314    </parameter>
315    <parameter>
316      <name>propertyMapping.gNumPixOLHi</name>
317      <label>G high outlier pixels</label>
318      <description>Number of outlier pixels per feature with intensity &gt; upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.</description>
319      <class>java.lang.String</class>
320      <value>\gNumPixOLHi\</value>
321    </parameter>
322    <parameter>
323      <name>propertyMapping.gIsFeatPopnOL</name>
324      <label>G population outlier</label>
325      <description>Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier.</description>
326      <class>java.lang.String</class>
327      <value>\gIsFeatPopnOL\</value>
328    </parameter>
329    <parameter>
330      <name>propertyMapping.gBGMeanSignal</name>
331      <label>G mean background</label>
332      <description>Mean local background signal (local to corresponding feature) computed per channel.</description>
333      <class>java.lang.String</class>
334      <value>\gBGMeanSignal\</value>
335    </parameter>
336    <parameter>
337      <name>propertyMapping.gBGSubSignal</name>
338      <label>G net signal</label>
339      <description>The net green signal following the subtraction of the background from the raw mean green signal.</description>
340      <class>java.lang.String</class>
341      <value>\gNetSignal\</value>
342    </parameter>
343    <parameter>
344      <name>rowColumnMapping</name>
345      <label>Row</label>
346      <description>Mapping that picks the spot's row coordinate from the data columns. This column is only used when the raw data is connected to an array design which uses the COORDINATES method for identifying features. In all other cases, the value is stored as is.For example: \Row\</description>
347      <class>java.lang.String</class>
348      <value>\Row\</value>
349    </parameter>
350    <parameter>
351      <name>propertyMapping.gNumPixOLLo</name>
352      <label>G low outlier pixels</label>
353      <description>Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.</description>
354      <class>java.lang.String</class>
355      <value>\gNumPixOLLo\</value>
356    </parameter>
357    <parameter>
358      <name>xColumnMapping</name>
359      <label>X</label>
360      <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
361      <class>java.lang.String</class>
362      <value>\PositionX\</value>
363    </parameter>
364  </configuration>
365</configfile>
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