Changeset 2975 for trunk/data


Ignore:
Timestamp:
Nov 29, 2006, 12:14:09 PM (15 years ago)
Author:
Nicklas Nordborg
Message:

Updated configuration files with correct column mappings.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/data/plugin_configfile.xml

    r2959 r2975  
    11<?xml version="1.0" encoding="UTF-8"?>
    2 <!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd">
    3 <!--
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    5   Copyright (C) Authors contributing to this file.
    6 
    7   This file is part of BASE - BioArray Software Environment.
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    24 -->
    25 <configfile>
     2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
    263  <configuration pluginClassName="net.sf.basedb.plugins.PlateFlatFileImporter">
    274    <configname>384_wells plate import</configname>
    285    <description>This configuration is for the Plate importer plugin when to import 384-well plates.</description>
    296    <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 />
     12    </parameter>
     13    <parameter>
     14      <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>
     17      <class>java.lang.String</class>
     18      <value>\oligo_id\</value>
     19    </parameter>
     20    <parameter>
     21      <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>
     24      <class>java.lang.String</class>
     25      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
     26    </parameter>
     27    <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>
     42      <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>
     45      <class>java.lang.String</class>
     46      <value>\t</value>
     47    </parameter>
     48    <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>
     56      <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>
     59      <class>java.lang.String</class>
     60      <value>\384_column\</value>
     61    </parameter>
     62    <parameter>
    3063      <name>nameColumnMapping</name>
    31       <label>nameColumnMapping</label>
     64      <label>Plate number/name</label>
     65      <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
    3266      <class>java.lang.String</class>
    3367      <value>\384_number\</value>
    3468    </parameter>
    3569    <parameter>
    36       <name>reporterColumnMapping</name>
    37       <label>reporterColumnMapping</label>
    38       <class>java.lang.String</class>
    39       <value>\oligo_id\</value>
    40     </parameter>
    41     <parameter>
    42       <name>dataHeaderRegexp</name>
    43       <label>dataHeaderRegexp</label>
    44       <class>java.lang.String</class>
    45       <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
    46     </parameter>
    47     <parameter>
    48       <name>dataSplitterRegexp</name>
    49       <label>dataSplitterRegexp</label>
    50       <class>java.lang.String</class>
    51       <value>\t</value>
    52     </parameter>
    53     <parameter>
    54       <name>columnColumnMapping</name>
    55       <label>columnColumnMapping</label>
    56       <class>java.lang.String</class>
    57       <value>\384_column\</value>
     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 />
    5896    </parameter>
    5997    <parameter>
    6098      <name>rowColumnMapping</name>
    61       <label>rowColumnMapping</label>
     99      <label>Row</label>
     100      <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
    62101      <class>java.lang.String</class>
    63102      <value>\384_row\</value>
     
    68107    <description>This configuration is for importing reporters from the same text file as 384well plates are imported from.</description>
    69108    <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>
    70144      <name>nameColumnMapping</name>
    71       <label>nameColumnMapping</label>
     145      <label>Name</label>
     146      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
    72147      <class>java.lang.String</class>
    73148      <value>\oligo_id\</value>
    74149    </parameter>
    75150    <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 />
     170    </parameter>
     171    <parameter>
     172      <name>descriptionColumnMapping</name>
     173      <label>Description</label>
     174      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
     175      <class>java.lang.String</class>
     176      <value>\description_Ensembl*\</value>
     177    </parameter>
     178    <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 />
     184    </parameter>
     185    <parameter>
     186      <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>
     189      <class>java.lang.String</class>
     190      <value>\oligo_id\</value>
     191    </parameter>
     192    <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>
    76228      <name>dataHeaderRegexp</name>
    77       <label>dataHeaderRegexp</label>
     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>
    78231      <class>java.lang.String</class>
    79232      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
     
    81234    <parameter>
    82235      <name>dataSplitterRegexp</name>
    83       <label>dataSplitterRegexp</label>
     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>
    84238      <class>java.lang.String</class>
    85239      <value>\t</value>
    86240    </parameter>
    87241    <parameter>
    88       <name>descriptionColumnMapping</name>
    89       <label>descriptionColumnMapping</label>
    90       <class>java.lang.String</class>
    91       <value>\description_Ensembl*\</value>
    92     </parameter>
    93     <parameter>
    94       <name>symbolColumnMapping</name>
    95       <label>symbolColumnMapping</label>
    96       <class>java.lang.String</class>
    97       <value>\gene_symbol_Ensembl*\</value>
    98     </parameter>
    99     <parameter>
    100       <name>reporterIdColumnMapping</name>
    101       <label>reporterIdColumnMapping</label>
    102       <class>java.lang.String</class>
    103       <value>\oligo_id\</value>
     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 />
    104310    </parameter>
    105311    <parameter>
    106312      <name>extendedColumnMapping.sequence</name>
    107       <label>extendedColumnMapping.sequence</label>
     313      <label>Sequence</label>
     314      <description>The nucleotide sequence of the reporter</description>
    108315      <class>java.lang.String</class>
    109316      <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 />
    110324    </parameter>
    111325  </configuration>
     
    116330      <name>maxDataColumns</name>
    117331      <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>
    118333      <class />
    119334      <value />
     
    122337      <name>extendedColumnMapping.locusLink</name>
    123338      <label>LocusLink</label>
     339      <description />
    124340      <class />
    125341      <value />
     
    128344      <name>trimQuotes</name>
    129345      <label>Remove quotes</label>
     346      <description>If true quotes (" or ') around data value will be removed.</description>
    130347      <class>java.lang.Boolean</class>
    131348      <value>true</value>
    132349    </parameter>
    133350    <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>
    134358      <name>scoreColumnMapping</name>
    135359      <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>
    136361      <class />
    137362      <value />
     
    140365      <name>nameColumnMapping</name>
    141366      <label>Name</label>
     367      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
    142368      <class>java.lang.String</class>
    143369      <value>\Name\</value>
     
    146372      <name>extendedColumnMapping.markers</name>
    147373      <label>Markers</label>
     374      <description />
    148375      <class />
    149376      <value />
     
    152379      <name>extendedColumnMapping.vector</name>
    153380      <label>Vector</label>
     381      <description>The vector from which the reporter is derived</description>
    154382      <class />
    155383      <value />
     
    158386      <name>extendedColumnMapping.nid</name>
    159387      <label>NID</label>
     388      <description />
    160389      <class />
    161390      <value />
     
    164393      <name>descriptionColumnMapping</name>
    165394      <label>Description</label>
     395      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
    166396      <class />
    167397      <value />
     
    170400      <name>headerRegexp</name>
    171401      <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>
    172403      <class />
    173404      <value />
     
    176407      <name>reporterIdColumnMapping</name>
    177408      <label>Reporter ID</label>
     409      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
    178410      <class>java.lang.String</class>
    179411      <value>\ID\</value>
     
    182414      <name>symbolColumnMapping</name>
    183415      <label>Gene symbol</label>
     416      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
    184417      <class />
    185418      <value />
     
    188421      <name>extendedColumnMapping.antibiotics</name>
    189422      <label>Antibiotics</label>
     423      <description />
     424      <class />
     425      <value />
     426    </parameter>
     427    <parameter>
     428      <name>extendedColumnMapping.omim</name>
     429      <label>OMIM</label>
     430      <description />
    190431      <class />
    191432      <value />
     
    194435      <name>extendedColumnMapping.chromosome</name>
    195436      <label>Chromosome</label>
     437      <description>The chromosome from which the reporter is derived</description>
    196438      <class />
    197439      <value />
     
    200442      <name>reporterType</name>
    201443      <label>Reporter type</label>
    202       <class />
    203       <value />
    204     </parameter>
    205     <parameter>
    206       <name>extendedColumnMapping.omim</name>
    207       <label>OMIM</label>
     444      <description>The reporter type assigned to the imported reporters</description>
    208445      <class />
    209446      <value />
     
    212449      <name>dataHeaderRegexp</name>
    213450      <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>
    214452      <class>java.lang.String</class>
    215453      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
     
    218456      <name>dataSplitterRegexp</name>
    219457      <label>Data splitter</label>
     458      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    220459      <class>java.lang.String</class>
    221460      <value>\t</value>
     
    224463      <name>extendedColumnMapping.length</name>
    225464      <label>Length</label>
     465      <description>The length of the sequence</description>
    226466      <class />
    227467      <value />
     
    230470      <name>extendedColumnMapping.tissue</name>
    231471      <label>Tissue</label>
     472      <description>The tissue from which the reporter is derived</description>
    232473      <class />
    233474      <value />
     
    236477      <name>extendedColumnMapping.accession</name>
    237478      <label>Accession</label>
     479      <description />
    238480      <class />
    239481      <value />
     
    242484      <name>minDataColumns</name>
    243485      <label>Min data columns</label>
     486      <description>The minimum number of columns for a line to be counted as a data line.</description>
    244487      <class />
    245488      <value />
     
    248491      <name>ignoreRegexp</name>
    249492      <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>
    250501      <class />
    251502      <value />
     
    254505      <name>extendedColumnMapping.library</name>
    255506      <label>Library</label>
     507      <description>The library from which the reporter is derived</description>
    256508      <class />
    257509      <value />
     
    260512      <name>extendedColumnMapping.clusterId</name>
    261513      <label>Cluster ID</label>
     514      <description>A unique identifier for a Unigene entry</description>
    262515      <class />
    263516      <value />
     
    266519      <name>dataFooterRegexp</name>
    267520      <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>
     522      <class />
     523      <value />
     524    </parameter>
     525    <parameter>
     526      <name>extendedColumnMapping.cytoband</name>
     527      <label>Cytoband</label>
     528      <description>The cytoband from which the reporter is derived</description>
    268529      <class />
    269530      <value />
     
    272533      <name>extendedColumnMapping.sequence</name>
    273534      <label>Sequence</label>
     535      <description>The nucleotide sequence of the reporter</description>
    274536      <class />
    275537      <value />
     
    278540      <name>extendedColumnMapping.species</name>
    279541      <label>Species</label>
    280       <class />
    281       <value />
    282     </parameter>
    283     <parameter>
    284       <name>extendedColumnMapping.cytoband</name>
    285       <label>Cytoband</label>
     542      <description>The organism from which the reporter is derived</description>
    286543      <class />
    287544      <value />
     
    293550Block mapping is used in this configuration.</description>
    294551    <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>
    295559      <name>dataHeaderRegexp</name>
    296       <label>dataHeaderRegexp</label>
     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>
    297562      <class>java.lang.String</class>
    298563      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
    299564    </parameter>
    300565    <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>
    301573      <name>dataSplitterRegexp</name>
    302       <label>dataSplitterRegexp</label>
     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>
    303576      <class>java.lang.String</class>
    304577      <value>\t</value>
    305578    </parameter>
    306579    <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>
    307587      <name>columnColumnMapping</name>
    308       <label>columnColumnMapping</label>
     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>
    309590      <class>java.lang.String</class>
    310591      <value>\Column\</value>
    311592    </parameter>
    312593    <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>
    313629      <name>reporterIdColumnMapping</name>
    314       <label>reporterIdColumnMapping</label>
     630      <label>Reporter ID</label>
     631      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
    315632      <class>java.lang.String</class>
    316633      <value>\ID\</value>
    317634    </parameter>
    318635    <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>
    319643      <name>blockColumnMapping</name>
    320       <label>blockColumnMapping</label>
     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>
    321646      <class>java.lang.String</class>
    322647      <value>\Block\</value>
     
    324649    <parameter>
    325650      <name>rowColumnMapping</name>
    326       <label>rowColumnMapping</label>
     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>
    327653      <class>java.lang.String</class>
    328654      <value>\Row\</value>
     
    336662      <name>yColumnMapping</name>
    337663      <label>Y</label>
     664      <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
    338665      <class>java.lang.String</class>
    339666      <value>\Y\</value>
     667    </parameter>
     668    <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 />
     674    </parameter>
     675    <parameter>
     676      <name>propertyMapping.flags</name>
     677      <label>Flags</label>
     678      <description>Flags</description>
     679      <class>java.lang.String</class>
     680      <value>\Flags\</value>
    340681    </parameter>
    341682    <parameter>
    342683      <name>propertyMapping.ch2BgMean</name>
    343684      <label>Channel 2 background mean</label>
     685      <description>The mean of the background intensity in channel 2</description>
    344686      <class>java.lang.String</class>
    345687      <value>\B532 Mean\</value>
    346     </parameter>
    347     <parameter>
    348       <name>propertyMapping.flags</name>
    349       <label>Flags</label>
    350       <class>java.lang.String</class>
    351       <value>\Flags\</value>
    352688    </parameter>
    353689    <parameter>
    354690      <name>propertyMapping.mValue</name>
    355691      <label>M value</label>
    356       <class>java.lang.String</class>
    357       <value>\Log Ratio (532/635)\</value>
     692      <description>M value</description>
     693      <class>java.lang.String</class>
     694      <value>\Log Ratio (635/532)\</value>
    358695    </parameter>
    359696    <parameter>
    360697      <name>trimQuotes</name>
    361698      <label>Remove quotes</label>
     699      <description>If true quotes (" or ') around data value will be removed.</description>
    362700      <class>java.lang.Boolean</class>
    363701      <value>true</value>
    364702    </parameter>
    365703    <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>
    366711      <name>propertyMapping.diameter</name>
    367712      <label>Spot diameter</label>
     713      <description>The diameter of the spot in pixels</description>
    368714      <class>java.lang.String</class>
    369715      <value>\Dia.\</value>
     
    372718      <name>propertyMapping.ch2PercSat</name>
    373719      <label>Percent saturated pixels</label>
     720      <description>Percentage of saturated pixels in channel 2</description>
    374721      <class>java.lang.String</class>
    375722      <value>\F532 % Sat.\</value>
     
    378725      <name>propertyMapping.ch1FgSd</name>
    379726      <label>Channel 1 foreground standard deviation</label>
     727      <description>The standard deviation of the foreground intensity in channel 1</description>
    380728      <class>java.lang.String</class>
    381729      <value>\F635 SD\</value>
     
    384732      <name>propertyMapping.ch2PercSd1</name>
    385733      <label>Percent pixels within 1 standard deviation</label>
     734      <description>Percentage of pixels within 1 standard deviation in channel 2</description>
    386735      <class>java.lang.String</class>
    387736      <value>\% &gt; B532+1SD\</value>
     
    390739      <name>propertyMapping.fgPixels</name>
    391740      <label>Foreground pixels</label>
     741      <description>Number of foreground pixels</description>
    392742      <class>java.lang.String</class>
    393743      <value>\F Pixels\</value>
     
    396746      <name>propertyMapping.ch2FgSd</name>
    397747      <label>Channel 2 foreground standard deviation</label>
     748      <description>The standard deviation of the foreground intensity in channel 2</description>
    398749      <class>java.lang.String</class>
    399750      <value>\F532 SD\</value>
     
    402753      <name>propertyMapping.ch2BgSd</name>
    403754      <label>Channel 2 background standard deviation</label>
     755      <description>The standard deviation of the background intensity in channel 2</description>
    404756      <class>java.lang.String</class>
    405757      <value>\B532 SD\</value>
     758    </parameter>
     759    <parameter>
     760      <name>reporterIdColumnMapping</name>
     761      <label>Reporter ID</label>
     762      <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
     763      <class>java.lang.String</class>
     764      <value>\ID\</value>
    406765    </parameter>
    407766    <parameter>
    408767      <name>headerRegexp</name>
    409768      <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>
    410770      <class>java.lang.String</class>
    411771      <value>"(.+)=(.*)"</value>
    412     </parameter>
    413     <parameter>
    414       <name>reporterIdColumnMapping</name>
    415       <label>Reporter ID</label>
    416       <class>java.lang.String</class>
    417       <value>\ID\</value>
    418772    </parameter>
    419773    <parameter>
    420774      <name>propertyMapping.ch1FgMedian</name>
    421775      <label>Channel 1 foreground median</label>
     776      <description>The median of the foreground intensity in channel 1</description>
    422777      <class>java.lang.String</class>
    423778      <value>\F635 Median\</value>
     
    426781      <name>propertyMapping.ch1BgMean</name>
    427782      <label>Channel 1 background mean</label>
     783      <description>The mean of the background intensity in channel 1</description>
    428784      <class>java.lang.String</class>
    429785      <value>\B635 Mean\</value>
     786    </parameter>
     787    <parameter>
     788      <name>rowColumnMapping</name>
     789      <label>Row</label>
     790      <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
     791      <class>java.lang.String</class>
     792      <value>\Row\</value>
    430793    </parameter>
    431794    <parameter>
    432795      <name>propertyMapping.ch2BgMedian</name>
    433796      <label>Channel 2 background median</label>
     797      <description>The median of the background intensity in channel 2</description>
    434798      <class>java.lang.String</class>
    435799      <value>\B532 Median\</value>
    436     </parameter>
    437     <parameter>
    438       <name>rowColumnMapping</name>
    439       <label>Row</label>
    440       <class>java.lang.String</class>
    441       <value>\Row\</value>
    442800    </parameter>
    443801    <parameter>
    444802      <name>propertyMapping.ch1BgMedian</name>
    445803      <label>Channel 1 background median</label>
     804      <description>The median of the background intensity in channel 1</description>
    446805      <class>java.lang.String</class>
    447806      <value>\B635 Median\</value>
     
    450809      <name>propertyMapping.ch2FgMean</name>
    451810      <label>Channel 2 foreground mean</label>
     811      <description>The mean of the foreground intensity in channel 2</description>
    452812      <class>java.lang.String</class>
    453813      <value>\F532 Mean\</value>
     
    456816      <name>propertyMapping.rgnR2</name>
    457817      <label>Rgn R2</label>
     818      <description>Rgn R2</description>
    458819      <class>java.lang.String</class>
    459820      <value>\Rgn R² (635/532)\</value>
     
    462823      <name>dataHeaderRegexp</name>
    463824      <label>Data header</label>
    464       <class>java.lang.String</class>
    465       <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*</value>
     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>
     828    </parameter>
     829    <parameter>
     830      <name>propertyMapping.ch2FgMedian</name>
     831      <label>Channel 2 foreground median</label>
     832      <description>The median of the foreground intensity in channel 2</description>
     833      <class>java.lang.String</class>
     834      <value>\F532 Median\</value>
    466835    </parameter>
    467836    <parameter>
    468837      <name>propertyMapping.ratiosSd</name>
    469838      <label>Standard deviation of ratios</label>
    470       <class>java.lang.String</class>
    471       <value>\Ratios SD (532/635)\</value>
    472     </parameter>
    473     <parameter>
    474       <name>propertyMapping.ch2FgMedian</name>
    475       <label>Channel 2 foreground median</label>
    476       <class>java.lang.String</class>
    477       <value>\F532 Median\</value>
     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>
    478842    </parameter>
    479843    <parameter>
    480844      <name>propertyMapping.ch1PercSat</name>
    481845      <label>Percent saturated pixels</label>
     846      <description>Percentage of saturated pixels in channel 1</description>
    482847      <class>java.lang.String</class>
    483848      <value>\F635 % Sat.\</value>
     
    486851      <name>dataSplitterRegexp</name>
    487852      <label>Data splitter</label>
     853      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    488854      <class>java.lang.String</class>
    489855      <value>\t</value>
     
    492858      <name>columnColumnMapping</name>
    493859      <label>Column</label>
     860      <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
    494861      <class>java.lang.String</class>
    495862      <value>\Column\</value>
     
    498865      <name>propertyMapping.bgPixels</name>
    499866      <label>Background pixels</label>
     867      <description>Number of background pixels</description>
    500868      <class>java.lang.String</class>
    501869      <value>\B Pixels\</value>
     
    504872      <name>propertyMapping.ch1PercSd2</name>
    505873      <label>Percent pixels within 2 standard deviations</label>
     874      <description>Percentage of pixels within 2 standard deviations in channel 1</description>
    506875      <class>java.lang.String</class>
    507876      <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 />
    508884    </parameter>
    509885    <parameter>
    510886      <name>propertyMapping.ch1FgMean</name>
    511887      <label>Channel 1 foreground mean</label>
     888      <description>The mean of the foreground intensity in channel 1</description>
    512889      <class>java.lang.String</class>
    513890      <value>\F635 Mean\</value>
     
    516893      <name>xColumnMapping</name>
    517894      <label>X</label>
     895      <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
    518896      <class>java.lang.String</class>
    519897      <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 />
    520905    </parameter>
    521906    <parameter>
    522907      <name>propertyMapping.ch1BgSd</name>
    523908      <label>Channel 1 background standard deviation</label>
     909      <description>The standard deviation of the background intensity in channel 1</description>
    524910      <class>java.lang.String</class>
    525911      <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 />
    526919    </parameter>
    527920    <parameter>
    528921      <name>propertyMapping.rgnRatio</name>
    529922      <label>Rgn ratio</label>
     923      <description>Rgn ratio</description>
    530924      <class>java.lang.String</class>
    531925      <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 />
    532940    </parameter>
    533941    <parameter>
    534942      <name>propertyMapping.ch1PercSd1</name>
    535943      <label>Percent pixels within 1 standard deviation</label>
     944      <description>Percentage of pixels within 1 standard deviation in channel 1</description>
    536945      <class>java.lang.String</class>
    537946      <value>\% &gt; B635+1SD\</value>
     
    540949      <name>rawDataType</name>
    541950      <label>Raw data type</label>
     951      <description>The type of raw data that this importer will import.</description>
    542952      <class>java.lang.String</class>
    543953      <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 />
    544961    </parameter>
    545962    <parameter>
    546963      <name>propertyMapping.ch2PercSd2</name>
    547964      <label>Percent pixels within 2 standard deviations</label>
     965      <description>Percentage of pixels within 2 standard deviations in channel 2</description>
    548966      <class>java.lang.String</class>
    549967      <value>\% &gt; B532+2SD\</value>
     
    552970      <name>blockColumnMapping</name>
    553971      <label>Block</label>
     972      <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
    554973      <class>java.lang.String</class>
    555974      <value>\Block\</value>
     
    563982      <name>yColumnMapping</name>
    564983      <label>Y</label>
     984      <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
    565985      <class>java.lang.String</class>
    566986      <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 />
    567994    </parameter>
    568995    <parameter>
    569996      <name>propertyMapping.ch2BgMean</name>
    570997      <label>Channel 2 background mean</label>
     998      <description>The mean of the background intensity in channel 2</description>
    571999      <class>java.lang.String</class>
    5721000      <value>\B635 Mean\</value>
     
    5751003      <name>propertyMapping.flags</name>
    5761004      <label>Flags</label>
     1005      <description>Flags</description>
    5771006      <class>java.lang.String</class>
    5781007      <value>\Flags\</value>
     
    5811010      <name>propertyMapping.mValue</name>
    5821011      <label>M value</label>
     1012      <description>M value</description>
    5831013      <class>java.lang.String</class>
    5841014      <value>\Log Ratio (532/635)\</value>
     
    5871017      <name>trimQuotes</name>
    5881018      <label>Remove quotes</label>
     1019      <description>If true quotes (" or ') around data value will be removed.</description>
    5891020      <class>java.lang.Boolean</class>
    5901021      <value>true</value>
    5911022    </parameter>
    5921023    <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>
    5931031      <name>propertyMapping.diameter</name>
    5941032      <label>Spot diameter</label>
     1033      <description>The diameter of the spot in pixels</description>
    5951034      <class>java.lang.String</class>
    5961035      <value>\Dia.\</value>
     
    5991038      <name>propertyMapping.ch2PercSat</name>
    6001039      <label>Percent saturated pixels</label>
     1040      <description>Percentage of saturated pixels in channel 2</description>
    6011041      <class>java.lang.String</class>
    6021042      <value>\F635 % Sat.\</value>
     
    6051045      <name>propertyMapping.ch1FgSd</name>
    6061046      <label>Channel 1 foreground standard deviation</label>
     1047      <description>The standard deviation of the foreground intensity in channel 1</description>
    6071048      <class>java.lang.String</class>
    6081049      <value>\F532 SD\</value>
     
    6111052      <name>propertyMapping.ch2PercSd1</name>
    6121053      <label>Percent pixels within 1 standard deviation</label>
     1054      <description>Percentage of pixels within 1 standard deviation in channel 2</description>
    6131055      <class>java.lang.String</class>
    6141056      <value>\% &gt; B635+1SD\</value>
     
    6171059      <name>propertyMapping.fgPixels</name>
    6181060      <label>Foreground pixels</label>
     1061      <description>Number of foreground pixels</description>
    6191062      <class>java.lang.String</class>
    6201063      <value>\F Pixels\</value>
     
    6231066      <name>propertyMapping.ch2FgSd</name>
    6241067      <label>Channel 2 foreground standard deviation</label>
     1068      <description>The standard deviation of the foreground intensity in channel 2</description>
    6251069      <class>java.lang.String</class>
    6261070      <value>\F635 SD\</value>
     
    6291073      <name>propertyMapping.ch2BgSd</name>
    6301074      <label>Channel 2 background standard deviation</label>
     1075      <description>The standard deviation of the background intensity in channel 2</description>
    6311076      <class>java.lang.String</class>
    6321077      <value>\B635 SD\</value>
     1078    </parameter>
     1079    <parameter>
     1080      <name>reporterIdColumnMapping</name>
     1081      <label>Reporter ID</label>
     1082      <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
     1083      <class>java.lang.String</class>
     1084      <value>\ID\</value>
    6331085    </parameter>
    6341086    <parameter>
    6351087      <name>headerRegexp</name>
    6361088      <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>
    6371090      <class>java.lang.String</class>
    6381091      <value>"(.+)=(.*)"</value>
    639     </parameter>
    640     <parameter>
    641       <name>reporterIdColumnMapping</name>
    642       <label>Reporter ID</label>
    643       <class>java.lang.String</class>
    644       <value>\ID\</value>
    6451092    </parameter>
    6461093    <parameter>
    6471094      <name>propertyMapping.ch1FgMedian</name>
    6481095      <label>Channel 1 foreground median</label>
     1096      <description>The median of the foreground intensity in channel 1</description>
    6491097      <class>java.lang.String</class>
    6501098      <value>\F532 Median\</value>
     
    6531101      <name>propertyMapping.ch1BgMean</name>
    6541102      <label>Channel 1 background mean</label>
     1103      <description>The mean of the background intensity in channel 1</description>
    6551104      <class>java.lang.String</class>
    6561105      <value>\B532 Mean\</value>
     
    6591108      <name>propertyMapping.ch2BgMedian</name>
    6601109      <label>Channel 2 background median</label>
     1110      <description>The median of the background intensity in channel 2</description>
    6611111      <class>java.lang.String</class>
    6621112      <value>\B635 Median\</value>
     
    6651115      <name>rowColumnMapping</name>
    6661116      <label>Row</label>
     1117      <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
    6671118      <class>java.lang.String</class>
    6681119      <value>\Row\</value>
     
    6711122      <name>propertyMapping.ch1BgMedian</name>
    6721123      <label>Channel 1 background median</label>
     1124      <description>The median of the background intensity in channel 1</description>
    6731125      <class>java.lang.String</class>
    6741126      <value>\B532 Median\</value>
     
    6771129      <name>propertyMapping.ch2FgMean</name>
    6781130      <label>Channel 2 foreground mean</label>
     1131      <description>The mean of the foreground intensity in channel 2</description>
    6791132      <class>java.lang.String</class>
    6801133      <value>\F635 Mean\</value>
     
    6831136      <name>propertyMapping.rgnR2</name>
    6841137      <label>Rgn R2</label>
     1138      <description>Rgn R2</description>
    6851139      <class>java.lang.String</class>
    6861140      <value>\Rgn R² (532/635)\</value>
     1141    </parameter>
     1142    <parameter>
     1143      <name>propertyMapping.ch2FgMedian</name>
     1144      <label>Channel 2 foreground median</label>
     1145      <description>The median of the foreground intensity in channel 2</description>
     1146      <class>java.lang.String</class>
     1147      <value>\F635 Median\</value>
    6871148    </parameter>
    6881149    <parameter>
    6891150      <name>dataHeaderRegexp</name>
    6901151      <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>
     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>
    6931155    </parameter>
    6941156    <parameter>
    6951157      <name>propertyMapping.ratiosSd</name>
    6961158      <label>Standard deviation of ratios</label>
     1159      <description>Standard deviation of the intensity ratios for all pixels</description>
    6971160      <class>java.lang.String</class>
    6981161      <value>\Ratios SD (532/635)\</value>
    699     </parameter>
    700     <parameter>
    701       <name>propertyMapping.ch2FgMedian</name>
    702       <label>Channel 2 foreground median</label>
    703       <class>java.lang.String</class>
    704       <value>\F635 Median\</value>
    7051162    </parameter>
    7061163    <parameter>
    7071164      <name>propertyMapping.ch1PercSat</name>
    7081165      <label>Percent saturated pixels</label>
     1166      <description>Percentage of saturated pixels in channel 1</description>
    7091167      <class>java.lang.String</class>
    7101168      <value>\F532 % Sat.\</value>
     
    7131171      <name>dataSplitterRegexp</name>
    7141172      <label>Data splitter</label>
     1173      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    7151174      <class>java.lang.String</class>
    7161175      <value>\t</value>
     
    7191178      <name>columnColumnMapping</name>
    7201179      <label>Column</label>
     1180      <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
    7211181      <class>java.lang.String</class>
    7221182      <value>\Column\</value>
     
    7251185      <name>propertyMapping.bgPixels</name>
    7261186      <label>Background pixels</label>
     1187      <description>Number of background pixels</description>
    7271188      <class>java.lang.String</class>
    7281189      <value>\B Pixels\</value>
     
    7311192      <name>propertyMapping.ch1PercSd2</name>
    7321193      <label>Percent pixels within 2 standard deviations</label>
     1194      <description>Percentage of pixels within 2 standard deviations in channel 1</description>
    7331195      <class>java.lang.String</class>
    7341196      <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 />
    7351204    </parameter>
    7361205    <parameter>
    7371206      <name>propertyMapping.ch1FgMean</name>
    7381207      <label>Channel 1 foreground mean</label>
     1208      <description>The mean of the foreground intensity in channel 1</description>
    7391209      <class>java.lang.String</class>
    7401210      <value>\F532 Mean\</value>
     
    7431213      <name>xColumnMapping</name>
    7441214      <label>X</label>
     1215      <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
    7451216      <class>java.lang.String</class>
    7461217      <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 />
    7471225    </parameter>
    7481226    <parameter>
    7491227      <name>propertyMapping.ch1BgSd</name>
    7501228      <label>Channel 1 background standard deviation</label>
     1229      <description>The standard deviation of the background intensity in channel 1</description>
    7511230      <class>java.lang.String</class>
    7521231      <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 />
    7531239    </parameter>
    7541240    <parameter>
    7551241      <name>propertyMapping.rgnRatio</name>
    7561242      <label>Rgn ratio</label>
     1243      <description>Rgn ratio</description>
    7571244      <class>java.lang.String</class>
    7581245      <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 />
    7591253    </parameter>
    7601254    <parameter>
    7611255      <name>propertyMapping.ch1PercSd1</name>
    7621256      <label>Percent pixels within 1 standard deviation</label>
     1257      <description>Percentage of pixels within 1 standard deviation in channel 1</description>
    7631258      <class>java.lang.String</class>
    7641259      <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 />
    7651267    </parameter>
    7661268    <parameter>
    7671269      <name>rawDataType</name>
    7681270      <label>Raw data type</label>
     1271      <description>The type of raw data that this importer will import.</description>
    7691272      <class>java.lang.String</class>
    7701273      <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 />
    7711281    </parameter>
    7721282    <parameter>
    7731283      <name>propertyMapping.ch2PercSd2</name>
    7741284      <label>Percent pixels within 2 standard deviations</label>
     1285      <description>Percentage of pixels within 2 standard deviations in channel 2</description>
    7751286      <class>java.lang.String</class>
    7761287      <value>\% &gt; B635+2SD\</value>
     
    7791290      <name>blockColumnMapping</name>
    7801291      <label>Block</label>
     1292      <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
    7811293      <class>java.lang.String</class>
    7821294      <value>\Block\</value>
     
    7871299    <description>This configuration is for the Plate importer plugin when to import 96-well plates.</description>
    7881300    <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 />
     1306    </parameter>
     1307    <parameter>
     1308      <name>reporterColumnMapping</name>
     1309      <label>Reporter ID</label>
     1310      <description>Mapping that picks the well's reporter id from the data columns. For example: \ID\</description>
     1311      <class>java.lang.String</class>
     1312      <value>\oligo_id\</value>
     1313    </parameter>
     1314    <parameter>
     1315      <name>dataHeaderRegexp</name>
     1316      <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>
     1318      <class>java.lang.String</class>
     1319      <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 />
     1327    </parameter>
     1328    <parameter>
     1329      <name>trimQuotes</name>
     1330      <label>Remove quotes</label>
     1331      <description>If true quotes (" or ') around data value will be removed.</description>
     1332      <class>java.lang.Boolean</class>
     1333      <value>true</value>
     1334    </parameter>
     1335    <parameter>
     1336      <name>dataSplitterRegexp</name>
     1337      <label>Data splitter</label>
     1338      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
     1339      <class>java.lang.String</class>
     1340      <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>
     1348    </parameter>
     1349    <parameter>
     1350      <name>columnColumnMapping</name>
     1351      <label>Column</label>
     1352      <description>Mapping that picks the well's column in the plate from the data columns. For example: \Column\</description>
     1353      <class>java.lang.String</class>
     1354      <value>\96_column\</value>
     1355    </parameter>
     1356    <parameter>
    7891357      <name>nameColumnMapping</name>
    7901358      <label>Plate number/name</label>
     1359      <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
    7911360      <class>java.lang.String</class>
    7921361      <value>\96_number\</value>
    7931362    </parameter>
    7941363    <parameter>
    795       <name>reporterColumnMapping</name>
    796       <label>Reporter ID</label>
    797       <class>java.lang.String</class>
    798       <value>\oligo_id\</value>
    799     </parameter>
    800     <parameter>
    801       <name>dataHeaderRegexp</name>
    802       <label>Data header</label>
    803       <class>java.lang.String</class>
    804       <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
    805     </parameter>
    806     <parameter>
    807       <name>trimQuotes</name>
    808       <label>Remove quotes</label>
    809       <class>java.lang.Boolean</class>
    810       <value>true</value>
    811     </parameter>
    812     <parameter>
    813       <name>dataSplitterRegexp</name>
    814       <label>Data splitter</label>
    815       <class>java.lang.String</class>
    816       <value>\t</value>
    817     </parameter>
    818     <parameter>
    819       <name>columnColumnMapping</name>
    820       <label>Column</label>
    821       <class>java.lang.String</class>
    822       <value>\96_column\</value>
     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 />
    8231390    </parameter>
    8241391    <parameter>
    8251392      <name>rowColumnMapping</name>
    8261393      <label>Row</label>
     1394      <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
    8271395      <class>java.lang.String</class>
    8281396      <value>\96_row\</value>
     
    8331401    <description>This configuration is for importing reporters from the same text file as 96well plates are imported from.</description>
    8341402    <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 />
     1415    </parameter>
     1416    <parameter>
     1417      <name>trimQuotes</name>
     1418      <label>Remove quotes</label>
     1419      <description>If true quotes (" or ') around data value will be removed.</description>
     1420      <class>java.lang.Boolean</class>
     1421      <value>true</value>
     1422    </parameter>
     1423    <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>
    8351438      <name>nameColumnMapping</name>
    8361439      <label>Name</label>
     1440      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
    8371441      <class>java.lang.String</class>
    8381442      <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 />
     1464    </parameter>
     1465    <parameter>
     1466      <name>descriptionColumnMapping</name>
     1467      <label>Description</label>
     1468      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
     1469      <class>java.lang.String</class>
     1470      <value>\description_Ensembl*\</value>
     1471    </parameter>
     1472    <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 />
     1478    </parameter>
     1479    <parameter>
     1480      <name>reporterIdColumnMapping</name>
     1481      <label>Reporter ID</label>
     1482      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
     1483      <class>java.lang.String</class>
     1484      <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 />
    8391520    </parameter>
    8401521    <parameter>
    8411522      <name>dataHeaderRegexp</name>
    8421523      <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>
    8431525      <class>java.lang.String</class>
    8441526      <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
    845     </parameter>
    846     <parameter>
    847       <name>trimQuotes</name>
    848       <label>Remove quotes</label>
    849       <class>java.lang.Boolean</class>
    850       <value>true</value>
    8511527    </parameter>
    8521528    <parameter>
    8531529      <name>dataSplitterRegexp</name>
    8541530      <label>Data splitter</label>
     1531      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
    8551532      <class>java.lang.String</class>
    8561533      <value>\t</value>
    8571534    </parameter>
    8581535    <parameter>
    859       <name>descriptionColumnMapping</name>
    860       <label>Description</label>
    861       <class>java.lang.String</class>
    862       <value>\description_Ensembl*\</value>
    863     </parameter>
    864     <parameter>
    865       <name>symbolColumnMapping</name>
    866       <label>Gene symbol</label>
    867       <class>java.lang.String</class>
    868       <value>\gene_symbol_Ensembl*\</value>
    869     </parameter>
    870     <parameter>
    871       <name>reporterIdColumnMapping</name>
    872       <label>Reporter ID</label>
    873       <class>java.lang.String</class>
    874       <value>\oligo_id\</value>
     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 />
    8751604    </parameter>
    8761605    <parameter>
    8771606      <name>extendedColumnMapping.sequence</name>
    8781607      <label>Sequence</label>
     1608      <description>The nucleotide sequence of the reporter</description>
    8791609      <class>java.lang.String</class>
    8801610      <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 />
    8811618    </parameter>
    8821619  </configuration>
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