DocBookSupport: reporter_importer_affymetrix2.xml

<?xml version="1.0" encoding="UTF-8"?>

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  Copyright (C) 2007 Jari Hakkinen

  This file is part of BASE - BioArray Software Environment.
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<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
  <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
    <configname>Affymetrix probe set importer 2</configname>
    <description>Works for HG-U133A</description>
    <parameter>
      <name>maxDataColumns</name>
      <label>Max data columns</label>
      <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>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.locusLink</name>
      <label>LocusLink</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>trimQuotes</name>
      <label>Remove quotes</label>
      <description>If true quotes (" or ') around data value will be removed.</description>
      <class>java.lang.Boolean</class>
      <value>true</value>
    </parameter>
    <parameter>
      <name>charset</name>
      <label>Character set</label>
      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
      <class>java.lang.String</class>
      <value>ISO-8859-1</value>
    </parameter>
    <parameter>
      <name>scoreColumnMapping</name>
      <label>Score</label>
      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>nameColumnMapping</name>
      <label>Name</label>
      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
      <class>java.lang.String</class>
      <value>\Probe Set ID\</value>
    </parameter>
    <parameter>
      <name>extendedColumnMapping.markers</name>
      <label>Markers</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.vector</name>
      <label>Vector</label>
      <description>The vector from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.nid</name>
      <label>NID</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>descriptionColumnMapping</name>
      <label>Description</label>
      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>headerRegexp</name>
      <label>Header</label>
      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>reporterIdColumnMapping</name>
      <label>Reporter ID</label>
      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
      <class>java.lang.String</class>
      <value>\Probe Set ID\</value>
    </parameter>
    <parameter>
      <name>symbolColumnMapping</name>
      <label>Gene symbol</label>
      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
      <class>java.lang.String</class>
      <value>\Gene Symbol\</value>
    </parameter>
    <parameter>
      <name>extendedColumnMapping.antibiotics</name>
      <label>Antibiotics</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.omim</name>
      <label>OMIM</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.chromosome</name>
      <label>Chromosome</label>
      <description>The chromosome from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>reporterType</name>
      <label>Reporter type</label>
      <description>The reporter type assigned to the imported reporters</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>dataHeaderRegexp</name>
      <label>Data header</label>
      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
      <class>java.lang.String</class>
      <value>"Probe Set ID"\t"GeneChip Array"\t.*</value>
    </parameter>
    <parameter>
      <name>dataSplitterRegexp</name>
      <label>Data splitter</label>
      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
      <class>java.lang.String</class>
      <value>\t</value>
    </parameter>
    <parameter>
      <name>extendedColumnMapping.length</name>
      <label>Length</label>
      <description>The length of the sequence</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.tissue</name>
      <label>Tissue</label>
      <description>The tissue from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.accession</name>
      <label>Accession</label>
      <description />
      <class />
      <value />
    </parameter>
    <parameter>
      <name>minDataColumns</name>
      <label>Min data columns</label>
      <description>The minimum number of columns for a line to be counted as a data line.</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>ignoreRegexp</name>
      <label>Ignore</label>
      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>reporterTypeColumnMapping</name>
      <label>Reporter type</label>
      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.library</name>
      <label>Library</label>
      <description>The library from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.clusterId</name>
      <label>Cluster ID</label>
      <description>A unique identifier for a Unigene entry</description>
      <class>java.lang.String</class>
      <value>\UniGene ID\</value>
    </parameter>
    <parameter>
      <name>decimalSeparator</name>
      <label>Decimal separator</label>
      <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
      <class>java.lang.String</class>
      <value>dot</value>
    </parameter>
    <parameter>
      <name>dataFooterRegexp</name>
      <label>Data footer</label>
      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.cytoband</name>
      <label>Cytoband</label>
      <description>The cytoband from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.sequence</name>
      <label>Sequence</label>
      <description>The nucleotide sequence of the reporter</description>
      <class />
      <value />
    </parameter>
    <parameter>
      <name>extendedColumnMapping.species</name>
      <label>Species</label>
      <description>The organism from which the reporter is derived</description>
      <class />
      <value />
    </parameter>
  </configuration>
</configfile>