Ignore:
Timestamp:
Dec 1, 2006, 3:00:14 PM (17 years ago)
Author:
Johan Enell
Message:

Merged log:branches/2.1#2846:2990 trunk.

File:
1 edited

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  • trunk/data/plugin_configfile.xml

    r2975 r2992  
    11<?xml version="1.0" encoding="UTF-8"?>
    2 <!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
     2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd">
     3<!--
     4  $Id:
     5  Copyright (C) Authors contributing to this file.
     6
     7  This file is part of BASE - BioArray Software Environment.
     8  Available at http://base.thep.lu.se/
     9
     10  BASE is free software; you can redistribute it and/or
     11  modify it under the terms of the GNU General Public License
     12  as published by the Free Software Foundation; either version 2
     13  of the License, or (at your option) any later version.
     14
     15  BASE is distributed in the hope that it will be useful,
     16  but WITHOUT ANY WARRANTY; without even the implied warranty of
     17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     18  GNU General Public License for more details.
     19
     20  You should have received a copy of the GNU General Public License
     21  along with this program; if not, write to the Free Software
     22  Foundation, Inc., 59 Temple Place - Suite 330,
     23  Boston, MA  02111-1307, USA.
     24-->
     25<configfile>
    326  <configuration pluginClassName="net.sf.basedb.plugins.PlateFlatFileImporter">
    427    <configname>384_wells plate import</configname>
    528    <description>This configuration is for the Plate importer plugin when to import 384-well plates.</description>
    629    <parameter>
    7       <name>maxDataColumns</name>
    8       <label>Max data columns</label>
    9       <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>
    10       <class />
    11       <value />
     30      <name>nameColumnMapping</name>
     31      <label>nameColumnMapping</label>
     32      <class>java.lang.String</class>
     33      <value>\384_number\</value>
    1234    </parameter>
    1335    <parameter>
    1436      <name>reporterColumnMapping</name>
    15       <label>Reporter ID</label>
    16       <description>Mapping that picks the well's reporter id from the data columns. For example: \ID\</description>
     37      <label>reporterColumnMapping</label>
    1738      <class>java.lang.String</class>
    1839      <value>\oligo_id\</value>
    … …  
    2041    <parameter>
    2142      <name>dataHeaderRegexp</name>
    22       <label>Data header</label>
    23       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
     43      <label>dataHeaderRegexp</label>
    2444      <class>java.lang.String</class>
    2545      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
    2646    </parameter>
    2747    <parameter>
    28       <name>barcodeColumnMapping</name>
    29       <label>Plate barcode</label>
    30       <description>Mapping that picks the plate barcode from the data columns. For example: \Barcode\</description>
    31       <class />
    32       <value />
    33     </parameter>
    34     <parameter>
    35       <name>trimQuotes</name>
    36       <label>Remove quotes</label>
    37       <description>If true quotes (" or ') around data value will be removed.</description>
    38       <class>java.lang.Boolean</class>
    39       <value>true</value>
    40     </parameter>
    41     <parameter>
    4248      <name>dataSplitterRegexp</name>
    43       <label>Data splitter</label>
    44       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
     49      <label>dataSplitterRegexp</label>
    4550      <class>java.lang.String</class>
    4651      <value>\t</value>
    4752    </parameter>
    4853    <parameter>
    49       <name>charset</name>
    50       <label>Character set</label>
    51       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    52       <class>java.lang.String</class>
    53       <value>ISO-8859-1</value>
    54     </parameter>
    55     <parameter>
    5654      <name>columnColumnMapping</name>
    57       <label>Column</label>
    58       <description>Mapping that picks the well's column in the plate from the data columns. For example: \Column\</description>
     55      <label>columnColumnMapping</label>
    5956      <class>java.lang.String</class>
    6057      <value>\384_column\</value>
    6158    </parameter>
    6259    <parameter>
    63       <name>nameColumnMapping</name>
    64       <label>Plate number/name</label>
    65       <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
    66       <class>java.lang.String</class>
    67       <value>\384_number\</value>
    68     </parameter>
    69     <parameter>
    70       <name>minDataColumns</name>
    71       <label>Min data columns</label>
    72       <description>The minimum number of columns for a line to be counted as a data line.</description>
    73       <class />
    74       <value />
    75     </parameter>
    76     <parameter>
    77       <name>ignoreRegexp</name>
    78       <label>Ignore</label>
    79       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    80       <class />
    81       <value />
    82     </parameter>
    83     <parameter>
    84       <name>dataFooterRegexp</name>
    85       <label>Data footer</label>
    86       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    87       <class />
    88       <value />
    89     </parameter>
    90     <parameter>
    91       <name>headerRegexp</name>
    92       <label>Header</label>
    93       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    94       <class />
    95       <value />
    96     </parameter>
    97     <parameter>
    9860      <name>rowColumnMapping</name>
    99       <label>Row</label>
    100       <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
     61      <label>rowColumnMapping</label>
    10162      <class>java.lang.String</class>
    10263      <value>\384_row\</value>
    … …  
    10768    <description>This configuration is for importing reporters from the same text file as 384well plates are imported from.</description>
    10869    <parameter>
    109       <name>maxDataColumns</name>
    110       <label>Max data columns</label>
    111       <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>
    112       <class />
    113       <value />
    114     </parameter>
    115     <parameter>
    116       <name>extendedColumnMapping.locusLink</name>
    117       <label>LocusLink</label>
    118       <description />
    119       <class />
    120       <value />
    121     </parameter>
    122     <parameter>
    123       <name>trimQuotes</name>
    124       <label>Remove quotes</label>
    125       <description>If true quotes (" or ') around data value will be removed.</description>
    126       <class>java.lang.Boolean</class>
    127       <value>true</value>
    128     </parameter>
    129     <parameter>
    130       <name>charset</name>
    131       <label>Character set</label>
    132       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    133       <class>java.lang.String</class>
    134       <value>ISO-8859-1</value>
    135     </parameter>
    136     <parameter>
    137       <name>scoreColumnMapping</name>
    138       <label>Score</label>
    139       <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
    140       <class />
    141       <value />
    142     </parameter>
    143     <parameter>
    14470      <name>nameColumnMapping</name>
    145       <label>Name</label>
    146       <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
     71      <label>nameColumnMapping</label>
    14772      <class>java.lang.String</class>
    14873      <value>\oligo_id\</value>
    14974    </parameter>
    15075    <parameter>
    151       <name>extendedColumnMapping.markers</name>
    152       <label>Markers</label>
    153       <description />
    154       <class />
    155       <value />
    156     </parameter>
    157     <parameter>
    158       <name>extendedColumnMapping.vector</name>
    159       <label>Vector</label>
    160       <description>The vector from which the reporter is derived</description>
    161       <class />
    162       <value />
    163     </parameter>
    164     <parameter>
    165       <name>extendedColumnMapping.nid</name>
    166       <label>NID</label>
    167       <description />
    168       <class />
    169       <value />
     76      <name>dataHeaderRegexp</name>
     77      <label>dataHeaderRegexp</label>
     78      <class>java.lang.String</class>
     79      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
     80    </parameter>
     81    <parameter>
     82      <name>dataSplitterRegexp</name>
     83      <label>dataSplitterRegexp</label>
     84      <class>java.lang.String</class>
     85      <value>\t</value>
    17086    </parameter>
    17187    <parameter>
    17288      <name>descriptionColumnMapping</name>
    173       <label>Description</label>
    174       <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
     89      <label>descriptionColumnMapping</label>
    17590      <class>java.lang.String</class>
    17691      <value>\description_Ensembl*\</value>
    17792    </parameter>
    17893    <parameter>
    179       <name>headerRegexp</name>
    180       <label>Header</label>
    181       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    182       <class />
    183       <value />
     94      <name>symbolColumnMapping</name>
     95      <label>symbolColumnMapping</label>
     96      <class>java.lang.String</class>
     97      <value>\gene_symbol_Ensembl*\</value>
    18498    </parameter>
    18599    <parameter>
    186100      <name>reporterIdColumnMapping</name>
    187       <label>Reporter ID</label>
    188       <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
     101      <label>reporterIdColumnMapping</label>
    189102      <class>java.lang.String</class>
    190103      <value>\oligo_id\</value>
    191104    </parameter>
    192105    <parameter>
    193       <name>symbolColumnMapping</name>
    194       <label>Gene symbol</label>
    195       <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
    196       <class>java.lang.String</class>
    197       <value>\gene_symbol_Ensembl*\</value>
    198     </parameter>
    199     <parameter>
    200       <name>extendedColumnMapping.antibiotics</name>
    201       <label>Antibiotics</label>
    202       <description />
    203       <class />
    204       <value />
    205     </parameter>
    206     <parameter>
    207       <name>extendedColumnMapping.omim</name>
    208       <label>OMIM</label>
    209       <description />
    210       <class />
    211       <value />
    212     </parameter>
    213     <parameter>
    214       <name>extendedColumnMapping.chromosome</name>
    215       <label>Chromosome</label>
    216       <description>The chromosome from which the reporter is derived</description>
    217       <class />
    218       <value />
    219     </parameter>
    220     <parameter>
    221       <name>reporterType</name>
    222       <label>Reporter type</label>
    223       <description>The reporter type assigned to the imported reporters</description>
    224       <class />
    225       <value />
    226     </parameter>
    227     <parameter>
    228       <name>dataHeaderRegexp</name>
    229       <label>Data header</label>
    230       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    231       <class>java.lang.String</class>
    232       <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
    233     </parameter>
    234     <parameter>
    235       <name>dataSplitterRegexp</name>
    236       <label>Data splitter</label>
    237       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    238       <class>java.lang.String</class>
    239       <value>\t</value>
    240     </parameter>
    241     <parameter>
    242       <name>extendedColumnMapping.length</name>
    243       <label>Length</label>
    244       <description>The length of the sequence</description>
    245       <class />
    246       <value />
    247     </parameter>
    248     <parameter>
    249       <name>extendedColumnMapping.tissue</name>
    250       <label>Tissue</label>
    251       <description>The tissue from which the reporter is derived</description>
    252       <class />
    253       <value />
    254     </parameter>
    255     <parameter>
    256       <name>extendedColumnMapping.accession</name>
    257       <label>Accession</label>
    258       <description />
    259       <class />
    260       <value />
    261     </parameter>
    262     <parameter>
    263       <name>minDataColumns</name>
    264       <label>Min data columns</label>
    265       <description>The minimum number of columns for a line to be counted as a data line.</description>
    266       <class />
    267       <value />
    268     </parameter>
    269     <parameter>
    270       <name>ignoreRegexp</name>
    271       <label>Ignore</label>
    272       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    273       <class />
    274       <value />
    275     </parameter>
    276     <parameter>
    277       <name>reporterTypeColumnMapping</name>
    278       <label>Reporter type</label>
    279       <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
    280       <class />
    281       <value />
    282     </parameter>
    283     <parameter>
    284       <name>extendedColumnMapping.library</name>
    285       <label>Library</label>
    286       <description>The library from which the reporter is derived</description>
    287       <class />
    288       <value />
    289     </parameter>
    290     <parameter>
    291       <name>extendedColumnMapping.clusterId</name>
    292       <label>Cluster ID</label>
    293       <description>A unique identifier for a Unigene entry</description>
    294       <class />
    295       <value />
    296     </parameter>
    297     <parameter>
    298       <name>dataFooterRegexp</name>
    299       <label>Data footer</label>
    300       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    301       <class />
    302       <value />
    303     </parameter>
    304     <parameter>
    305       <name>extendedColumnMapping.cytoband</name>
    306       <label>Cytoband</label>
    307       <description>The cytoband from which the reporter is derived</description>
    308       <class />
    309       <value />
    310     </parameter>
    311     <parameter>
    312106      <name>extendedColumnMapping.sequence</name>
    313       <label>Sequence</label>
    314       <description>The nucleotide sequence of the reporter</description>
     107      <label>extendedColumnMapping.sequence</label>
    315108      <class>java.lang.String</class>
    316109      <value>\oligo_sequence\</value>
    317     </parameter>
    318     <parameter>
    319       <name>extendedColumnMapping.species</name>
    320       <label>Species</label>
    321       <description>The organism from which the reporter is derived</description>
    322       <class />
    323       <value />
    324110    </parameter>
    325111  </configuration>
    … …  
    330116      <name>maxDataColumns</name>
    331117      <label>Max data columns</label>
    332       <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>
    333118      <class />
    334119      <value />
    … …  
    337122      <name>extendedColumnMapping.locusLink</name>
    338123      <label>LocusLink</label>
    339       <description />
    340124      <class />
    341125      <value />
    … …  
    344128      <name>trimQuotes</name>
    345129      <label>Remove quotes</label>
    346       <description>If true quotes (" or ') around data value will be removed.</description>
    347130      <class>java.lang.Boolean</class>
    348131      <value>true</value>
    349132    </parameter>
    350133    <parameter>
    351       <name>charset</name>
    352       <label>Character set</label>
    353       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    354       <class>java.lang.String</class>
    355       <value>ISO-8859-1</value>
    356     </parameter>
    357     <parameter>
    358134      <name>scoreColumnMapping</name>
    359135      <label>Score</label>
    360       <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
    361136      <class />
    362137      <value />
    … …  
    365140      <name>nameColumnMapping</name>
    366141      <label>Name</label>
    367       <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
    368142      <class>java.lang.String</class>
    369143      <value>\Name\</value>
    … …  
    372146      <name>extendedColumnMapping.markers</name>
    373147      <label>Markers</label>
    374       <description />
    375148      <class />
    376149      <value />
    … …  
    379152      <name>extendedColumnMapping.vector</name>
    380153      <label>Vector</label>
    381       <description>The vector from which the reporter is derived</description>
    382154      <class />
    383155      <value />
    … …  
    386158      <name>extendedColumnMapping.nid</name>
    387159      <label>NID</label>
    388       <description />
    389160      <class />
    390161      <value />
    … …  
    393164      <name>descriptionColumnMapping</name>
    394165      <label>Description</label>
    395       <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
    396166      <class />
    397167      <value />
    … …  
    400170      <name>headerRegexp</name>
    401171      <label>Header</label>
    402       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    403172      <class />
    404173      <value />
    … …  
    407176      <name>reporterIdColumnMapping</name>
    408177      <label>Reporter ID</label>
    409       <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
    410178      <class>java.lang.String</class>
    411179      <value>\ID\</value>
    … …  
    414182      <name>symbolColumnMapping</name>
    415183      <label>Gene symbol</label>
    416       <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
    417184      <class />
    418185      <value />
    … …  
    421188      <name>extendedColumnMapping.antibiotics</name>
    422189      <label>Antibiotics</label>
    423       <description />
     190      <class />
     191      <value />
     192    </parameter>
     193    <parameter>
     194      <name>extendedColumnMapping.chromosome</name>
     195      <label>Chromosome</label>
     196      <class />
     197      <value />
     198    </parameter>
     199    <parameter>
     200      <name>reporterType</name>
     201      <label>Reporter type</label>
    424202      <class />
    425203      <value />
    … …  
    428206      <name>extendedColumnMapping.omim</name>
    429207      <label>OMIM</label>
    430       <description />
    431       <class />
    432       <value />
    433     </parameter>
    434     <parameter>
    435       <name>extendedColumnMapping.chromosome</name>
    436       <label>Chromosome</label>
    437       <description>The chromosome from which the reporter is derived</description>
    438       <class />
    439       <value />
    440     </parameter>
    441     <parameter>
    442       <name>reporterType</name>
    443       <label>Reporter type</label>
    444       <description>The reporter type assigned to the imported reporters</description>
    445208      <class />
    446209      <value />
    … …  
    449212      <name>dataHeaderRegexp</name>
    450213      <label>Data header</label>
    451       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    452214      <class>java.lang.String</class>
    453215      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
    … …  
    456218      <name>dataSplitterRegexp</name>
    457219      <label>Data splitter</label>
    458       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    459220      <class>java.lang.String</class>
    460221      <value>\t</value>
    … …  
    463224      <name>extendedColumnMapping.length</name>
    464225      <label>Length</label>
    465       <description>The length of the sequence</description>
    466226      <class />
    467227      <value />
    … …  
    470230      <name>extendedColumnMapping.tissue</name>
    471231      <label>Tissue</label>
    472       <description>The tissue from which the reporter is derived</description>
    473232      <class />
    474233      <value />
    … …  
    477236      <name>extendedColumnMapping.accession</name>
    478237      <label>Accession</label>
    479       <description />
    480238      <class />
    481239      <value />
    … …  
    484242      <name>minDataColumns</name>
    485243      <label>Min data columns</label>
    486       <description>The minimum number of columns for a line to be counted as a data line.</description>
    487244      <class />
    488245      <value />
    … …  
    491248      <name>ignoreRegexp</name>
    492249      <label>Ignore</label>
    493       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    494       <class />
    495       <value />
    496     </parameter>
    497     <parameter>
    498       <name>reporterTypeColumnMapping</name>
    499       <label>Reporter type</label>
    500       <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
    501250      <class />
    502251      <value />
    … …  
    505254      <name>extendedColumnMapping.library</name>
    506255      <label>Library</label>
    507       <description>The library from which the reporter is derived</description>
    508256      <class />
    509257      <value />
    … …  
    512260      <name>extendedColumnMapping.clusterId</name>
    513261      <label>Cluster ID</label>
    514       <description>A unique identifier for a Unigene entry</description>
    515262      <class />
    516263      <value />
    … …  
    519266      <name>dataFooterRegexp</name>
    520267      <label>Data footer</label>
    521       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
     268      <class />
     269      <value />
     270    </parameter>
     271    <parameter>
     272      <name>extendedColumnMapping.sequence</name>
     273      <label>Sequence</label>
     274      <class />
     275      <value />
     276    </parameter>
     277    <parameter>
     278      <name>extendedColumnMapping.species</name>
     279      <label>Species</label>
    522280      <class />
    523281      <value />
    … …  
    526284      <name>extendedColumnMapping.cytoband</name>
    527285      <label>Cytoband</label>
    528       <description>The cytoband from which the reporter is derived</description>
    529       <class />
    530       <value />
    531     </parameter>
    532     <parameter>
    533       <name>extendedColumnMapping.sequence</name>
    534       <label>Sequence</label>
    535       <description>The nucleotide sequence of the reporter</description>
    536       <class />
    537       <value />
    538     </parameter>
    539     <parameter>
    540       <name>extendedColumnMapping.species</name>
    541       <label>Species</label>
    542       <description>The organism from which the reporter is derived</description>
    543286      <class />
    544287      <value />
    … …  
    550293Block mapping is used in this configuration.</description>
    551294    <parameter>
    552       <name>maxDataColumns</name>
    553       <label>Max data columns</label>
    554       <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>
    555       <class />
    556       <value />
    557     </parameter>
    558     <parameter>
    559295      <name>dataHeaderRegexp</name>
    560       <label>Data header</label>
    561       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
     296      <label>dataHeaderRegexp</label>
    562297      <class>java.lang.String</class>
    563298      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
    564299    </parameter>
    565300    <parameter>
    566       <name>trimQuotes</name>
    567       <label>Remove quotes</label>
    568       <description>If true quotes (" or ') around data value will be removed.</description>
    569       <class>java.lang.Boolean</class>
    570       <value>true</value>
    571     </parameter>
    572     <parameter>
    573301      <name>dataSplitterRegexp</name>
    574       <label>Data splitter</label>
    575       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
     302      <label>dataSplitterRegexp</label>
    576303      <class>java.lang.String</class>
    577304      <value>\t</value>
    578305    </parameter>
    579306    <parameter>
    580       <name>charset</name>
    581       <label>Character set</label>
    582       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    583       <class>java.lang.String</class>
    584       <value>ISO-8859-1</value>
    585     </parameter>
    586     <parameter>
    587307      <name>columnColumnMapping</name>
    588       <label>Column</label>
    589       <description>Mapping that picks the feature's column position in a block from the data columns. For example: \Column\</description>
     308      <label>columnColumnMapping</label>
    590309      <class>java.lang.String</class>
    591310      <value>\Column\</value>
    592311    </parameter>
    593312    <parameter>
    594       <name>metaGridXColumnMapping</name>
    595       <label>Meta grid X</label>
    596       <description>Mapping that picks the feature's meta grid X coordinate from the data columns. Required if you don't specify a block mapping. Example: \Meta grid X\</description>
    597       <class />
    598       <value />
    599     </parameter>
    600     <parameter>
    601       <name>metaGridYColumnMapping</name>
    602       <label>Meta grid Y</label>
    603       <description>Mapping that picks the feature's meta grid Y coordinate from the data columns. Required if you don't specify a block mapping. Example: \Meta grid Y\</description>
    604       <class />
    605       <value />
    606     </parameter>
    607     <parameter>
    608       <name>minDataColumns</name>
    609       <label>Min data columns</label>
    610       <description>The minimum number of columns for a line to be counted as a data line.</description>
    611       <class />
    612       <value />
    613     </parameter>
    614     <parameter>
    615       <name>ignoreRegexp</name>
    616       <label>Ignore</label>
    617       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    618       <class />
    619       <value />
    620     </parameter>
    621     <parameter>
    622       <name>dataFooterRegexp</name>
    623       <label>Data footer</label>
    624       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    625       <class />
    626       <value />
    627     </parameter>
    628     <parameter>
    629313      <name>reporterIdColumnMapping</name>
    630       <label>Reporter ID</label>
    631       <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
     314      <label>reporterIdColumnMapping</label>
    632315      <class>java.lang.String</class>
    633316      <value>\ID\</value>
    634317    </parameter>
    635318    <parameter>
    636       <name>headerRegexp</name>
    637       <label>Header</label>
    638       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    639       <class />
    640       <value />
    641     </parameter>
    642     <parameter>
    643319      <name>blockColumnMapping</name>
    644       <label>Block</label>
    645       <description>Mapping that picks the feature's block number from the data columns. You must specify either this mapping or mappings for the meta coordinates. Example: \Block\</description>
     320      <label>blockColumnMapping</label>
    646321      <class>java.lang.String</class>
    647322      <value>\Block\</value>
    … …  
    649324    <parameter>
    650325      <name>rowColumnMapping</name>
    651       <label>Row</label>
    652       <description>Mapping that picks the feature's row position in a block from the data columns. For example: \Row\</description>
     326      <label>rowColumnMapping</label>
    653327      <class>java.lang.String</class>
    654328      <value>\Row\</value>
    … …  
    662336      <name>yColumnMapping</name>
    663337      <label>Y</label>
    664       <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
    665338      <class>java.lang.String</class>
    666339      <value>\Y\</value>
    667340    </parameter>
    668341    <parameter>
    669       <name>maxDataColumns</name>
    670       <label>Max data columns</label>
    671       <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>
    672       <class />
    673       <value />
     342      <name>propertyMapping.ch2BgMean</name>
     343      <label>Channel 2 background mean</label>
     344      <class>java.lang.String</class>
     345      <value>\B532 Mean\</value>
    674346    </parameter>
    675347    <parameter>
    676348      <name>propertyMapping.flags</name>
    677349      <label>Flags</label>
    678       <description>Flags</description>
    679350      <class>java.lang.String</class>
    680351      <value>\Flags\</value>
    681     </parameter>
    682     <parameter>
    683       <name>propertyMapping.ch2BgMean</name>
    684       <label>Channel 2 background mean</label>
    685       <description>The mean of the background intensity in channel 2</description>
    686       <class>java.lang.String</class>
    687       <value>\B532 Mean\</value>
    688352    </parameter>
    689353    <parameter>
    690354      <name>propertyMapping.mValue</name>
    691355      <label>M value</label>
    692       <description>M value</description>
    693       <class>java.lang.String</class>
    694       <value>\Log Ratio (635/532)\</value>
     356      <class>java.lang.String</class>
     357      <value>\Log Ratio (532/635)\</value>
    695358    </parameter>
    696359    <parameter>
    697360      <name>trimQuotes</name>
    698361      <label>Remove quotes</label>
    699       <description>If true quotes (" or ') around data value will be removed.</description>
    700362      <class>java.lang.Boolean</class>
    701363      <value>true</value>
    702364    </parameter>
    703365    <parameter>
    704       <name>charset</name>
    705       <label>Character set</label>
    706       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    707       <class>java.lang.String</class>
    708       <value>ISO-8859-1</value>
    709     </parameter>
    710     <parameter>
    711366      <name>propertyMapping.diameter</name>
    712367      <label>Spot diameter</label>
    713       <description>The diameter of the spot in pixels</description>
    714368      <class>java.lang.String</class>
    715369      <value>\Dia.\</value>
    … …  
    718372      <name>propertyMapping.ch2PercSat</name>
    719373      <label>Percent saturated pixels</label>
    720       <description>Percentage of saturated pixels in channel 2</description>
    721374      <class>java.lang.String</class>
    722375      <value>\F532 % Sat.\</value>
    … …  
    725378      <name>propertyMapping.ch1FgSd</name>
    726379      <label>Channel 1 foreground standard deviation</label>
    727       <description>The standard deviation of the foreground intensity in channel 1</description>
    728380      <class>java.lang.String</class>
    729381      <value>\F635 SD\</value>
    … …  
    732384      <name>propertyMapping.ch2PercSd1</name>
    733385      <label>Percent pixels within 1 standard deviation</label>
    734       <description>Percentage of pixels within 1 standard deviation in channel 2</description>
    735386      <class>java.lang.String</class>
    736387      <value>\% &gt; B532+1SD\</value>
    … …  
    739390      <name>propertyMapping.fgPixels</name>
    740391      <label>Foreground pixels</label>
    741       <description>Number of foreground pixels</description>
    742392      <class>java.lang.String</class>
    743393      <value>\F Pixels\</value>
    … …  
    746396      <name>propertyMapping.ch2FgSd</name>
    747397      <label>Channel 2 foreground standard deviation</label>
    748       <description>The standard deviation of the foreground intensity in channel 2</description>
    749398      <class>java.lang.String</class>
    750399      <value>\F532 SD\</value>
    … …  
    753402      <name>propertyMapping.ch2BgSd</name>
    754403      <label>Channel 2 background standard deviation</label>
    755       <description>The standard deviation of the background intensity in channel 2</description>
    756404      <class>java.lang.String</class>
    757405      <value>\B532 SD\</value>
     406    </parameter>
     407    <parameter>
     408      <name>headerRegexp</name>
     409      <label>Header</label>
     410      <class>java.lang.String</class>
     411      <value>"(.+)=(.*)"</value>
    758412    </parameter>
    759413    <parameter>
    760414      <name>reporterIdColumnMapping</name>
    761415      <label>Reporter ID</label>
    762       <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
    763416      <class>java.lang.String</class>
    764417      <value>\ID\</value>
    765     </parameter>
    766     <parameter>
    767       <name>headerRegexp</name>
    768       <label>Header</label>
    769       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    770       <class>java.lang.String</class>
    771       <value>"(.+)=(.*)"</value>
    772418    </parameter>
    773419    <parameter>
    774420      <name>propertyMapping.ch1FgMedian</name>
    775421      <label>Channel 1 foreground median</label>
    776       <description>The median of the foreground intensity in channel 1</description>
    777422      <class>java.lang.String</class>
    778423      <value>\F635 Median\</value>
    … …  
    781426      <name>propertyMapping.ch1BgMean</name>
    782427      <label>Channel 1 background mean</label>
    783       <description>The mean of the background intensity in channel 1</description>
    784428      <class>java.lang.String</class>
    785429      <value>\B635 Mean\</value>
     430    </parameter>
     431    <parameter>
     432      <name>propertyMapping.ch2BgMedian</name>
     433      <label>Channel 2 background median</label>
     434      <class>java.lang.String</class>
     435      <value>\B532 Median\</value>
    786436    </parameter>
    787437    <parameter>
    788438      <name>rowColumnMapping</name>
    789439      <label>Row</label>
    790       <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
    791440      <class>java.lang.String</class>
    792441      <value>\Row\</value>
    793     </parameter>
    794     <parameter>
    795       <name>propertyMapping.ch2BgMedian</name>
    796       <label>Channel 2 background median</label>
    797       <description>The median of the background intensity in channel 2</description>
    798       <class>java.lang.String</class>
    799       <value>\B532 Median\</value>
    800442    </parameter>
    801443    <parameter>
    802444      <name>propertyMapping.ch1BgMedian</name>
    803445      <label>Channel 1 background median</label>
    804       <description>The median of the background intensity in channel 1</description>
    805446      <class>java.lang.String</class>
    806447      <value>\B635 Median\</value>
    … …  
    809450      <name>propertyMapping.ch2FgMean</name>
    810451      <label>Channel 2 foreground mean</label>
    811       <description>The mean of the foreground intensity in channel 2</description>
    812452      <class>java.lang.String</class>
    813453      <value>\F532 Mean\</value>
    … …  
    816456      <name>propertyMapping.rgnR2</name>
    817457      <label>Rgn R2</label>
    818       <description>Rgn R2</description>
    819458      <class>java.lang.String</class>
    820459      <value>\Rgn R² (635/532)\</value>
    … …  
    823462      <name>dataHeaderRegexp</name>
    824463      <label>Data header</label>
    825       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    826       <class>java.lang.String</class>
    827       <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(635\/532\)".*</value>
     464      <class>java.lang.String</class>
     465      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*</value>
     466    </parameter>
     467    <parameter>
     468      <name>propertyMapping.ratiosSd</name>
     469      <label>Standard deviation of ratios</label>
     470      <class>java.lang.String</class>
     471      <value>\Ratios SD (532/635)\</value>
    828472    </parameter>
    829473    <parameter>
    830474      <name>propertyMapping.ch2FgMedian</name>
    831475      <label>Channel 2 foreground median</label>
    832       <description>The median of the foreground intensity in channel 2</description>
    833476      <class>java.lang.String</class>
    834477      <value>\F532 Median\</value>
    835     </parameter>
    836     <parameter>
    837       <name>propertyMapping.ratiosSd</name>
    838       <label>Standard deviation of ratios</label>
    839       <description>Standard deviation of the intensity ratios for all pixels</description>
    840       <class>java.lang.String</class>
    841       <value>\Ratios SD (635/532)\</value>
    842478    </parameter>
    843479    <parameter>
    844480      <name>propertyMapping.ch1PercSat</name>
    845481      <label>Percent saturated pixels</label>
    846       <description>Percentage of saturated pixels in channel 1</description>
    847482      <class>java.lang.String</class>
    848483      <value>\F635 % Sat.\</value>
    … …  
    851486      <name>dataSplitterRegexp</name>
    852487      <label>Data splitter</label>
    853       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    854488      <class>java.lang.String</class>
    855489      <value>\t</value>
    … …  
    858492      <name>columnColumnMapping</name>
    859493      <label>Column</label>
    860       <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
    861494      <class>java.lang.String</class>
    862495      <value>\Column\</value>
    … …  
    865498      <name>propertyMapping.bgPixels</name>
    866499      <label>Background pixels</label>
    867       <description>Number of background pixels</description>
    868500      <class>java.lang.String</class>
    869501      <value>\B Pixels\</value>
    … …  
    872504      <name>propertyMapping.ch1PercSd2</name>
    873505      <label>Percent pixels within 2 standard deviations</label>
    874       <description>Percentage of pixels within 2 standard deviations in channel 1</description>
    875506      <class>java.lang.String</class>
    876507      <value>\% &gt; B635+2SD\</value>
    877     </parameter>
    878     <parameter>
    879       <name>metaGridXColumnMapping</name>
    880       <label>MetaGridX</label>
    881       <description>Mapping that picks the spot's meta-Grid X-axis from the data columns. For example: \Meta grid X\</description>
    882       <class />
    883       <value />
    884508    </parameter>
    885509    <parameter>
    886510      <name>propertyMapping.ch1FgMean</name>
    887511      <label>Channel 1 foreground mean</label>
    888       <description>The mean of the foreground intensity in channel 1</description>
    889512      <class>java.lang.String</class>
    890513      <value>\F635 Mean\</value>
    … …  
    893516      <name>xColumnMapping</name>
    894517      <label>X</label>
    895       <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
    896518      <class>java.lang.String</class>
    897519      <value>\X\</value>
    898     </parameter>
    899     <parameter>
    900       <name>metaGridYColumnMapping</name>
    901       <label>MetaGridY</label>
    902       <description>Mapping that picks the spot's meta-Grid Y-axis from the data columns. For example: \Meta grid Y\</description>
    903       <class />
    904       <value />
    905520    </parameter>
    906521    <parameter>
    907522      <name>propertyMapping.ch1BgSd</name>
    908523      <label>Channel 1 background standard deviation</label>
    909       <description>The standard deviation of the background intensity in channel 1</description>
    910524      <class>java.lang.String</class>
    911525      <value>\B635 SD\</value>
    912     </parameter>
    913     <parameter>
    914       <name>minDataColumns</name>
    915       <label>Min data columns</label>
    916       <description>The minimum number of columns for a line to be counted as a data line.</description>
    917       <class />
    918       <value />
    919526    </parameter>
    920527    <parameter>
    921528      <name>propertyMapping.rgnRatio</name>
    922529      <label>Rgn ratio</label>
    923       <description>Rgn ratio</description>
    924530      <class>java.lang.String</class>
    925531      <value>\Rgn Ratio (635/532)\</value>
    926     </parameter>
    927     <parameter>
    928       <name>ignoreRegexp</name>
    929       <label>Ignore</label>
    930       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    931       <class />
    932       <value />
    933     </parameter>
    934     <parameter>
    935       <name>propertyMapping.CV</name>
    936       <label>CV</label>
    937       <description>CV</description>
    938       <class />
    939       <value />
    940532    </parameter>
    941533    <parameter>
    942534      <name>propertyMapping.ch1PercSd1</name>
    943535      <label>Percent pixels within 1 standard deviation</label>
    944       <description>Percentage of pixels within 1 standard deviation in channel 1</description>
    945536      <class>java.lang.String</class>
    946537      <value>\% &gt; B635+1SD\</value>
    … …  
    949540      <name>rawDataType</name>
    950541      <label>Raw data type</label>
    951       <description>The type of raw data that this importer will import.</description>
    952542      <class>java.lang.String</class>
    953543      <value>genepix</value>
    954     </parameter>
    955     <parameter>
    956       <name>dataFooterRegexp</name>
    957       <label>Data footer</label>
    958       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    959       <class />
    960       <value />
    961544    </parameter>
    962545    <parameter>
    963546      <name>propertyMapping.ch2PercSd2</name>
    964547      <label>Percent pixels within 2 standard deviations</label>
    965       <description>Percentage of pixels within 2 standard deviations in channel 2</description>
    966548      <class>java.lang.String</class>
    967549      <value>\% &gt; B532+2SD\</value>
    … …  
    970552      <name>blockColumnMapping</name>
    971553      <label>Block</label>
    972       <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
    973554      <class>java.lang.String</class>
    974555      <value>\Block\</value>
    … …  
    982563      <name>yColumnMapping</name>
    983564      <label>Y</label>
    984       <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
    985565      <class>java.lang.String</class>
    986566      <value>\Y\</value>
    987     </parameter>
    988     <parameter>
    989       <name>maxDataColumns</name>
    990       <label>Max data columns</label>
    991       <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>
    992       <class />
    993       <value />
    994567    </parameter>
    995568    <parameter>
    996569      <name>propertyMapping.ch2BgMean</name>
    997570      <label>Channel 2 background mean</label>
    998       <description>The mean of the background intensity in channel 2</description>
    999571      <class>java.lang.String</class>
    1000572      <value>\B635 Mean\</value>
    … …  
    1003575      <name>propertyMapping.flags</name>
    1004576      <label>Flags</label>
    1005       <description>Flags</description>
    1006577      <class>java.lang.String</class>
    1007578      <value>\Flags\</value>
    … …  
    1010581      <name>propertyMapping.mValue</name>
    1011582      <label>M value</label>
    1012       <description>M value</description>
    1013583      <class>java.lang.String</class>
    1014584      <value>\Log Ratio (532/635)\</value>
    … …  
    1017587      <name>trimQuotes</name>
    1018588      <label>Remove quotes</label>
    1019       <description>If true quotes (" or ') around data value will be removed.</description>
    1020589      <class>java.lang.Boolean</class>
    1021590      <value>true</value>
    1022591    </parameter>
    1023592    <parameter>
    1024       <name>charset</name>
    1025       <label>Character set</label>
    1026       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    1027       <class>java.lang.String</class>
    1028       <value>ISO-8859-1</value>
    1029     </parameter>
    1030     <parameter>
    1031593      <name>propertyMapping.diameter</name>
    1032594      <label>Spot diameter</label>
    1033       <description>The diameter of the spot in pixels</description>
    1034595      <class>java.lang.String</class>
    1035596      <value>\Dia.\</value>
    … …  
    1038599      <name>propertyMapping.ch2PercSat</name>
    1039600      <label>Percent saturated pixels</label>
    1040       <description>Percentage of saturated pixels in channel 2</description>
    1041601      <class>java.lang.String</class>
    1042602      <value>\F635 % Sat.\</value>
    … …  
    1045605      <name>propertyMapping.ch1FgSd</name>
    1046606      <label>Channel 1 foreground standard deviation</label>
    1047       <description>The standard deviation of the foreground intensity in channel 1</description>
    1048607      <class>java.lang.String</class>
    1049608      <value>\F532 SD\</value>
    … …  
    1052611      <name>propertyMapping.ch2PercSd1</name>
    1053612      <label>Percent pixels within 1 standard deviation</label>
    1054       <description>Percentage of pixels within 1 standard deviation in channel 2</description>
    1055613      <class>java.lang.String</class>
    1056614      <value>\% &gt; B635+1SD\</value>
    … …  
    1059617      <name>propertyMapping.fgPixels</name>
    1060618      <label>Foreground pixels</label>
    1061       <description>Number of foreground pixels</description>
    1062619      <class>java.lang.String</class>
    1063620      <value>\F Pixels\</value>
    … …  
    1066623      <name>propertyMapping.ch2FgSd</name>
    1067624      <label>Channel 2 foreground standard deviation</label>
    1068       <description>The standard deviation of the foreground intensity in channel 2</description>
    1069625      <class>java.lang.String</class>
    1070626      <value>\F635 SD\</value>
    … …  
    1073629      <name>propertyMapping.ch2BgSd</name>
    1074630      <label>Channel 2 background standard deviation</label>
    1075       <description>The standard deviation of the background intensity in channel 2</description>
    1076631      <class>java.lang.String</class>
    1077632      <value>\B635 SD\</value>
     633    </parameter>
     634    <parameter>
     635      <name>headerRegexp</name>
     636      <label>Header</label>
     637      <class>java.lang.String</class>
     638      <value>"(.+)=(.*)"</value>
    1078639    </parameter>
    1079640    <parameter>
    1080641      <name>reporterIdColumnMapping</name>
    1081642      <label>Reporter ID</label>
    1082       <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
    1083643      <class>java.lang.String</class>
    1084644      <value>\ID\</value>
    1085     </parameter>
    1086     <parameter>
    1087       <name>headerRegexp</name>
    1088       <label>Header</label>
    1089       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    1090       <class>java.lang.String</class>
    1091       <value>"(.+)=(.*)"</value>
    1092645    </parameter>
    1093646    <parameter>
    1094647      <name>propertyMapping.ch1FgMedian</name>
    1095648      <label>Channel 1 foreground median</label>
    1096       <description>The median of the foreground intensity in channel 1</description>
    1097649      <class>java.lang.String</class>
    1098650      <value>\F532 Median\</value>
    … …  
    1101653      <name>propertyMapping.ch1BgMean</name>
    1102654      <label>Channel 1 background mean</label>
    1103       <description>The mean of the background intensity in channel 1</description>
    1104655      <class>java.lang.String</class>
    1105656      <value>\B532 Mean\</value>
    … …  
    1108659      <name>propertyMapping.ch2BgMedian</name>
    1109660      <label>Channel 2 background median</label>
    1110       <description>The median of the background intensity in channel 2</description>
    1111661      <class>java.lang.String</class>
    1112662      <value>\B635 Median\</value>
    … …  
    1115665      <name>rowColumnMapping</name>
    1116666      <label>Row</label>
    1117       <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
    1118667      <class>java.lang.String</class>
    1119668      <value>\Row\</value>
    … …  
    1122671      <name>propertyMapping.ch1BgMedian</name>
    1123672      <label>Channel 1 background median</label>
    1124       <description>The median of the background intensity in channel 1</description>
    1125673      <class>java.lang.String</class>
    1126674      <value>\B532 Median\</value>
    … …  
    1129677      <name>propertyMapping.ch2FgMean</name>
    1130678      <label>Channel 2 foreground mean</label>
    1131       <description>The mean of the foreground intensity in channel 2</description>
    1132679      <class>java.lang.String</class>
    1133680      <value>\F635 Mean\</value>
    … …  
    1136683      <name>propertyMapping.rgnR2</name>
    1137684      <label>Rgn R2</label>
    1138       <description>Rgn R2</description>
    1139685      <class>java.lang.String</class>
    1140686      <value>\Rgn R² (532/635)\</value>
     687    </parameter>
     688    <parameter>
     689      <name>dataHeaderRegexp</name>
     690      <label>Data header</label>
     691      <class>java.lang.String</class>
     692      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(635\/532\)".*</value>
     693    </parameter>
     694    <parameter>
     695      <name>propertyMapping.ratiosSd</name>
     696      <label>Standard deviation of ratios</label>
     697      <class>java.lang.String</class>
     698      <value>\Ratios SD (532/635)\</value>
    1141699    </parameter>
    1142700    <parameter>
    1143701      <name>propertyMapping.ch2FgMedian</name>
    1144702      <label>Channel 2 foreground median</label>
    1145       <description>The median of the foreground intensity in channel 2</description>
    1146703      <class>java.lang.String</class>
    1147704      <value>\F635 Median\</value>
    1148     </parameter>
    1149     <parameter>
    1150       <name>dataHeaderRegexp</name>
    1151       <label>Data header</label>
    1152       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    1153       <class>java.lang.String</class>
    1154       <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*</value>
    1155     </parameter>
    1156     <parameter>
    1157       <name>propertyMapping.ratiosSd</name>
    1158       <label>Standard deviation of ratios</label>
    1159       <description>Standard deviation of the intensity ratios for all pixels</description>
    1160       <class>java.lang.String</class>
    1161       <value>\Ratios SD (532/635)\</value>
    1162705    </parameter>
    1163706    <parameter>
    1164707      <name>propertyMapping.ch1PercSat</name>
    1165708      <label>Percent saturated pixels</label>
    1166       <description>Percentage of saturated pixels in channel 1</description>
    1167709      <class>java.lang.String</class>
    1168710      <value>\F532 % Sat.\</value>
    … …  
    1171713      <name>dataSplitterRegexp</name>
    1172714      <label>Data splitter</label>
    1173       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    1174715      <class>java.lang.String</class>
    1175716      <value>\t</value>
    … …  
    1178719      <name>columnColumnMapping</name>
    1179720      <label>Column</label>
    1180       <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
    1181721      <class>java.lang.String</class>
    1182722      <value>\Column\</value>
    … …  
    1185725      <name>propertyMapping.bgPixels</name>
    1186726      <label>Background pixels</label>
    1187       <description>Number of background pixels</description>
    1188727      <class>java.lang.String</class>
    1189728      <value>\B Pixels\</value>
    … …  
    1192731      <name>propertyMapping.ch1PercSd2</name>
    1193732      <label>Percent pixels within 2 standard deviations</label>
    1194       <description>Percentage of pixels within 2 standard deviations in channel 1</description>
    1195733      <class>java.lang.String</class>
    1196734      <value>\% &gt; B532+2SD\</value>
    1197     </parameter>
    1198     <parameter>
    1199       <name>metaGridXColumnMapping</name>
    1200       <label>MetaGridX</label>
    1201       <description>Mapping that picks the spot's meta-Grid X-axis from the data columns. For example: \Meta grid X\</description>
    1202       <class />
    1203       <value />
    1204735    </parameter>
    1205736    <parameter>
    1206737      <name>propertyMapping.ch1FgMean</name>
    1207738      <label>Channel 1 foreground mean</label>
    1208       <description>The mean of the foreground intensity in channel 1</description>
    1209739      <class>java.lang.String</class>
    1210740      <value>\F532 Mean\</value>
    … …  
    1213743      <name>xColumnMapping</name>
    1214744      <label>X</label>
    1215       <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
    1216745      <class>java.lang.String</class>
    1217746      <value>\X\</value>
    1218     </parameter>
    1219     <parameter>
    1220       <name>metaGridYColumnMapping</name>
    1221       <label>MetaGridY</label>
    1222       <description>Mapping that picks the spot's meta-Grid Y-axis from the data columns. For example: \Meta grid Y\</description>
    1223       <class />
    1224       <value />
    1225747    </parameter>
    1226748    <parameter>
    1227749      <name>propertyMapping.ch1BgSd</name>
    1228750      <label>Channel 1 background standard deviation</label>
    1229       <description>The standard deviation of the background intensity in channel 1</description>
    1230751      <class>java.lang.String</class>
    1231752      <value>\B532 SD\</value>
    1232     </parameter>
    1233     <parameter>
    1234       <name>minDataColumns</name>
    1235       <label>Min data columns</label>
    1236       <description>The minimum number of columns for a line to be counted as a data line.</description>
    1237       <class />
    1238       <value />
    1239753    </parameter>
    1240754    <parameter>
    1241755      <name>propertyMapping.rgnRatio</name>
    1242756      <label>Rgn ratio</label>
    1243       <description>Rgn ratio</description>
    1244757      <class>java.lang.String</class>
    1245758      <value>\Rgn Ratio (532/635)\</value>
    1246     </parameter>
    1247     <parameter>
    1248       <name>ignoreRegexp</name>
    1249       <label>Ignore</label>
    1250       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    1251       <class />
    1252       <value />
    1253759    </parameter>
    1254760    <parameter>
    1255761      <name>propertyMapping.ch1PercSd1</name>
    1256762      <label>Percent pixels within 1 standard deviation</label>
    1257       <description>Percentage of pixels within 1 standard deviation in channel 1</description>
    1258763      <class>java.lang.String</class>
    1259764      <value>\% &gt; B532+1SD\</value>
    1260     </parameter>
    1261     <parameter>
    1262       <name>propertyMapping.CV</name>
    1263       <label>CV</label>
    1264       <description>CV</description>
    1265       <class />
    1266       <value />
    1267765    </parameter>
    1268766    <parameter>
    1269767      <name>rawDataType</name>
    1270768      <label>Raw data type</label>
    1271       <description>The type of raw data that this importer will import.</description>
    1272769      <class>java.lang.String</class>
    1273770      <value>genepix</value>
    1274     </parameter>
    1275     <parameter>
    1276       <name>dataFooterRegexp</name>
    1277       <label>Data footer</label>
    1278       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    1279       <class />
    1280       <value />
    1281771    </parameter>
    1282772    <parameter>
    1283773      <name>propertyMapping.ch2PercSd2</name>
    1284774      <label>Percent pixels within 2 standard deviations</label>
    1285       <description>Percentage of pixels within 2 standard deviations in channel 2</description>
    1286775      <class>java.lang.String</class>
    1287776      <value>\% &gt; B635+2SD\</value>
    … …  
    1290779      <name>blockColumnMapping</name>
    1291780      <label>Block</label>
    1292       <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
    1293781      <class>java.lang.String</class>
    1294782      <value>\Block\</value>
    … …  
    1299787    <description>This configuration is for the Plate importer plugin when to import 96-well plates.</description>
    1300788    <parameter>
    1301       <name>maxDataColumns</name>
    1302       <label>Max data columns</label>
    1303       <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>
    1304       <class />
    1305       <value />
     789      <name>nameColumnMapping</name>
     790      <label>Plate number/name</label>
     791      <class>java.lang.String</class>
     792      <value>\96_number\</value>
    1306793    </parameter>
    1307794    <parameter>
    1308795      <name>reporterColumnMapping</name>
    1309796      <label>Reporter ID</label>
    1310       <description>Mapping that picks the well's reporter id from the data columns. For example: \ID\</description>
    1311797      <class>java.lang.String</class>
    1312798      <value>\oligo_id\</value>
    … …  
    1315801      <name>dataHeaderRegexp</name>
    1316802      <label>Data header</label>
    1317       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    1318803      <class>java.lang.String</class>
    1319804      <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
    1320     </parameter>
    1321     <parameter>
    1322       <name>barcodeColumnMapping</name>
    1323       <label>Plate barcode</label>
    1324       <description>Mapping that picks the plate barcode from the data columns. For example: \Barcode\</description>
    1325       <class />
    1326       <value />
    1327805    </parameter>
    1328806    <parameter>
    1329807      <name>trimQuotes</name>
    1330808      <label>Remove quotes</label>
    1331       <description>If true quotes (" or ') around data value will be removed.</description>
    1332809      <class>java.lang.Boolean</class>
    1333810      <value>true</value>
    … …  
    1336813      <name>dataSplitterRegexp</name>
    1337814      <label>Data splitter</label>
    1338       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    1339815      <class>java.lang.String</class>
    1340816      <value>\t</value>
    1341     </parameter>
    1342     <parameter>
    1343       <name>charset</name>
    1344       <label>Character set</label>
    1345       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    1346       <class>java.lang.String</class>
    1347       <value>ISO-8859-1</value>
    1348817    </parameter>
    1349818    <parameter>
    1350819      <name>columnColumnMapping</name>
    1351820      <label>Column</label>
    1352       <description>Mapping that picks the well's column in the plate from the data columns. For example: \Column\</description>
    1353821      <class>java.lang.String</class>
    1354822      <value>\96_column\</value>
    1355     </parameter>
    1356     <parameter>
    1357       <name>nameColumnMapping</name>
    1358       <label>Plate number/name</label>
    1359       <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
    1360       <class>java.lang.String</class>
    1361       <value>\96_number\</value>
    1362     </parameter>
    1363     <parameter>
    1364       <name>minDataColumns</name>
    1365       <label>Min data columns</label>
    1366       <description>The minimum number of columns for a line to be counted as a data line.</description>
    1367       <class />
    1368       <value />
    1369     </parameter>
    1370     <parameter>
    1371       <name>ignoreRegexp</name>
    1372       <label>Ignore</label>
    1373       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    1374       <class />
    1375       <value />
    1376     </parameter>
    1377     <parameter>
    1378       <name>dataFooterRegexp</name>
    1379       <label>Data footer</label>
    1380       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    1381       <class />
    1382       <value />
    1383     </parameter>
    1384     <parameter>
    1385       <name>headerRegexp</name>
    1386       <label>Header</label>
    1387       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    1388       <class />
    1389       <value />
    1390823    </parameter>
    1391824    <parameter>
    1392825      <name>rowColumnMapping</name>
    1393826      <label>Row</label>
    1394       <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
    1395827      <class>java.lang.String</class>
    1396828      <value>\96_row\</value>
    … …  
    1401833    <description>This configuration is for importing reporters from the same text file as 96well plates are imported from.</description>
    1402834    <parameter>
    1403       <name>maxDataColumns</name>
    1404       <label>Max data columns</label>
    1405       <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>
    1406       <class />
    1407       <value />
    1408     </parameter>
    1409     <parameter>
    1410       <name>extendedColumnMapping.locusLink</name>
    1411       <label>LocusLink</label>
    1412       <description />
    1413       <class />
    1414       <value />
     835      <name>nameColumnMapping</name>
     836      <label>Name</label>
     837      <class>java.lang.String</class>
     838      <value>\oligo_id\</value>
     839    </parameter>
     840    <parameter>
     841      <name>dataHeaderRegexp</name>
     842      <label>Data header</label>
     843      <class>java.lang.String</class>
     844      <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
    1415845    </parameter>
    1416846    <parameter>
    1417847      <name>trimQuotes</name>
    1418848      <label>Remove quotes</label>
    1419       <description>If true quotes (" or ') around data value will be removed.</description>
    1420849      <class>java.lang.Boolean</class>
    1421850      <value>true</value>
    1422851    </parameter>
    1423852    <parameter>
    1424       <name>charset</name>
    1425       <label>Character set</label>
    1426       <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
    1427       <class>java.lang.String</class>
    1428       <value>ISO-8859-1</value>
    1429     </parameter>
    1430     <parameter>
    1431       <name>scoreColumnMapping</name>
    1432       <label>Score</label>
    1433       <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
    1434       <class />
    1435       <value />
    1436     </parameter>
    1437     <parameter>
    1438       <name>nameColumnMapping</name>
    1439       <label>Name</label>
    1440       <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
    1441       <class>java.lang.String</class>
    1442       <value>\oligo_id\</value>
    1443     </parameter>
    1444     <parameter>
    1445       <name>extendedColumnMapping.markers</name>
    1446       <label>Markers</label>
    1447       <description />
    1448       <class />
    1449       <value />
    1450     </parameter>
    1451     <parameter>
    1452       <name>extendedColumnMapping.vector</name>
    1453       <label>Vector</label>
    1454       <description>The vector from which the reporter is derived</description>
    1455       <class />
    1456       <value />
    1457     </parameter>
    1458     <parameter>
    1459       <name>extendedColumnMapping.nid</name>
    1460       <label>NID</label>
    1461       <description />
    1462       <class />
    1463       <value />
     853      <name>dataSplitterRegexp</name>
     854      <label>Data splitter</label>
     855      <class>java.lang.String</class>
     856      <value>\t</value>
    1464857    </parameter>
    1465858    <parameter>
    1466859      <name>descriptionColumnMapping</name>
    1467860      <label>Description</label>
    1468       <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
    1469861      <class>java.lang.String</class>
    1470862      <value>\description_Ensembl*\</value>
    1471863    </parameter>
    1472864    <parameter>
    1473       <name>headerRegexp</name>
    1474       <label>Header</label>
    1475       <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
    1476       <class />
    1477       <value />
     865      <name>symbolColumnMapping</name>
     866      <label>Gene symbol</label>
     867      <class>java.lang.String</class>
     868      <value>\gene_symbol_Ensembl*\</value>
    1478869    </parameter>
    1479870    <parameter>
    1480871      <name>reporterIdColumnMapping</name>
    1481872      <label>Reporter ID</label>
    1482       <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
    1483873      <class>java.lang.String</class>
    1484874      <value>\oligo_id\</value>
    1485     </parameter>
    1486     <parameter>
    1487       <name>symbolColumnMapping</name>
    1488       <label>Gene symbol</label>
    1489       <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
    1490       <class>java.lang.String</class>
    1491       <value>\gene_symbol_Ensembl*\</value>
    1492     </parameter>
    1493     <parameter>
    1494       <name>extendedColumnMapping.antibiotics</name>
    1495       <label>Antibiotics</label>
    1496       <description />
    1497       <class />
    1498       <value />
    1499     </parameter>
    1500     <parameter>
    1501       <name>extendedColumnMapping.omim</name>
    1502       <label>OMIM</label>
    1503       <description />
    1504       <class />
    1505       <value />
    1506     </parameter>
    1507     <parameter>
    1508       <name>extendedColumnMapping.chromosome</name>
    1509       <label>Chromosome</label>
    1510       <description>The chromosome from which the reporter is derived</description>
    1511       <class />
    1512       <value />
    1513     </parameter>
    1514     <parameter>
    1515       <name>reporterType</name>
    1516       <label>Reporter type</label>
    1517       <description>The reporter type assigned to the imported reporters</description>
    1518       <class />
    1519       <value />
    1520     </parameter>
    1521     <parameter>
    1522       <name>dataHeaderRegexp</name>
    1523       <label>Data header</label>
    1524       <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
    1525       <class>java.lang.String</class>
    1526       <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
    1527     </parameter>
    1528     <parameter>
    1529       <name>dataSplitterRegexp</name>
    1530       <label>Data splitter</label>
    1531       <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    1532       <class>java.lang.String</class>
    1533       <value>\t</value>
    1534     </parameter>
    1535     <parameter>
    1536       <name>extendedColumnMapping.length</name>
    1537       <label>Length</label>
    1538       <description>The length of the sequence</description>
    1539       <class />
    1540       <value />
    1541     </parameter>
    1542     <parameter>
    1543       <name>extendedColumnMapping.tissue</name>
    1544       <label>Tissue</label>
    1545       <description>The tissue from which the reporter is derived</description>
    1546       <class />
    1547       <value />
    1548     </parameter>
    1549     <parameter>
    1550       <name>extendedColumnMapping.accession</name>
    1551       <label>Accession</label>
    1552       <description />
    1553       <class />
    1554       <value />
    1555     </parameter>
    1556     <parameter>
    1557       <name>minDataColumns</name>
    1558       <label>Min data columns</label>
    1559       <description>The minimum number of columns for a line to be counted as a data line.</description>
    1560       <class />
    1561       <value />
    1562     </parameter>
    1563     <parameter>
    1564       <name>ignoreRegexp</name>
    1565       <label>Ignore</label>
    1566       <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
    1567       <class />
    1568       <value />
    1569     </parameter>
    1570     <parameter>
    1571       <name>reporterTypeColumnMapping</name>
    1572       <label>Reporter type</label>
    1573       <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
    1574       <class />
    1575       <value />
    1576     </parameter>
    1577     <parameter>
    1578       <name>extendedColumnMapping.library</name>
    1579       <label>Library</label>
    1580       <description>The library from which the reporter is derived</description>
    1581       <class />
    1582       <value />
    1583     </parameter>
    1584     <parameter>
    1585       <name>extendedColumnMapping.clusterId</name>
    1586       <label>Cluster ID</label>
    1587       <description>A unique identifier for a Unigene entry</description>
    1588       <class />
    1589       <value />
    1590     </parameter>
    1591     <parameter>
    1592       <name>dataFooterRegexp</name>
    1593       <label>Data footer</label>
    1594       <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
    1595       <class />
    1596       <value />
    1597     </parameter>
    1598     <parameter>
    1599       <name>extendedColumnMapping.cytoband</name>
    1600       <label>Cytoband</label>
    1601       <description>The cytoband from which the reporter is derived</description>
    1602       <class />
    1603       <value />
    1604875    </parameter>
    1605876    <parameter>
    1606877      <name>extendedColumnMapping.sequence</name>
    1607878      <label>Sequence</label>
    1608       <description>The nucleotide sequence of the reporter</description>
    1609879      <class>java.lang.String</class>
    1610880      <value>\oligo_sequence\</value>
    1611     </parameter>
    1612     <parameter>
    1613       <name>extendedColumnMapping.species</name>
    1614       <label>Species</label>
    1615       <description>The organism from which the reporter is derived</description>
    1616       <class />
    1617       <value />
    1618881    </parameter>
    1619882  </configuration>
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