Changeset 565

Jan 31, 2008, 4:48:27 PM (13 years ago)
Martin Svensson

References #90 Added a default plugin configuration to come along with the jar-file and set the auto-installer to know there is configurations to install.

2 edited


  • trunk/net/sf/basedb/illumina/META-INF/base-configurations.xml

    r559 r565  
    237237    </parameter>
    238238  </configuration>
     239  <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxFeatureImporter">
     240    <configname>Features from BGX file</configname>
     241    <description>This is a standard configuration to import features from a BGX file.</description>
     242    <parameter>
     243      <name>trimQuotes</name>
     244      <label>Remove quotes</label>
     245      <description>If true quotes (" or ') around data value will be removed.</description>
     246      <class>java.lang.Boolean</class>
     247      <value>true</value>
     248    </parameter>
     249    <parameter>
     250      <name>dataHeaderRegexp</name>
     251      <label>Data header</label>
     252      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
     253      <class>java.lang.String</class>
     254      <value>\QSpecies  Source  Search_Key  Transcript  ILMN_Gene Source_Reference_ID RefSeq_ID Unigene_ID  Entrez_Gene_ID  GI  Accession Symbol  Protein_Product Probe_Id  Array_Address_Id  Probe_Type  Probe_Start Probe_Sequence  Chromosome  Probe_Chr_Orientation Probe_Coordinates Definition  Ontology_Component  Ontology_Process  Ontology_Function Synonyms  Obsolete_Probe_Id\E</value>
     255    </parameter>
     256    <parameter>
     257      <name>reporterIdColumnMapping</name>
     258      <label>Reporter ID</label>
     259      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
     260      <class>java.lang.String</class>
     261      <value>\Probe_Id\</value>
     262    </parameter>
     263    <parameter>
     264      <name>featureIdentification</name>
     265      <label>Identify features by</label>
     266      <description>Choose which method to use for identifying features:
     267COORDINATES: Use block, meta-grid, row and column coordinates
     268POSITION: Use a position number only
     269FEATURE_ID: Use the feature ID value (string)
     270In all cases, the identifier value must be unique.</description>
     271      <class>java.lang.String</class>
     272      <value>FEATURE_ID</value>
     273    </parameter>
     274    <parameter>
     275      <name>complexExpressions</name>
     276      <label>Complex column mappings</label>
     277      <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\'
     278allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description>
     279      <class>java.lang.String</class>
     280      <value>disallow</value>
     281    </parameter>
     282    <parameter>
     283      <name>charset</name>
     284      <label>Character set</label>
     285      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
     286      <class>java.lang.String</class>
     287      <value>ISO-8859-1</value>
     288    </parameter>
     289    <parameter>
     290      <name>featureIdColumnMapping</name>
     291      <label>Feature ID</label>
     292      <description>Mapping that picks the feature's ID from the data columns. This column is only used when the array design uses the FEATURE_ID method for identifying features. In the other cases, the value is just stored as it is.For example: \Feature ID\</description>
     293      <class>java.lang.String</class>
     294      <value>\Array_Address_Id\</value>
     295    </parameter>
     296    <parameter>
     297      <name>dataSplitterRegexp</name>
     298      <label>Data splitter</label>
     299      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
     300      <class>java.lang.String</class>
     301      <value>\t</value>
     302    </parameter>
     303    <parameter>
     304      <name>headerRegexp</name>
     305      <label>Header</label>
     306      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
     307      <class>java.lang.String</class>
     308      <value>(.+)=(.*)</value>
     309    </parameter>
     310  </configuration>
  • trunk/net/sf/basedb/illumina/META-INF/base-plugins.xml

    r546 r565  
    88  <pluginclass classname="net.sf.basedb.illumina.plugins.BgxFeatureImporter">
    99    <minbaseversion>2.6</minbaseversion>
    10     <hasconfigurations/>
     10    <hasconfigurations>yes</hasconfigurations>
    1111    </pluginclass>
    1212    <!-- 
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