source: extensions/net.sf.basedb.reggie/branches/2.15-stable/META-INF/extensions.xml @ 2507

<?xml version="1.0" encoding="UTF-8" ?>
<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about>
    <name>Reggie package</name>
    <description>
      A package for simplified registration of biosources
      and samples.
    </description>
    <version>2.15.3</version>
    <min-base-version>3.2.2</min-base-version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie</url>
  </about>

  <plugin-definition id="CaliperSampleNameExporter">
    <about>
      <name>Caliper sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        CSV file that can be used by the Caliper software. The
        exported file has one line for each non-empty well with
        five columns. Only the first two columns are used:
        Well coordinate, sample name.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperRunParametersExporter">
    <about>
      <name>Caliper run parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperRunParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperLibPrepParametersExporter">
    <about>
      <name>Caliper library preparation parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="QubitSampleNameExporter">
    <about>
      <name>Qubit sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        tab-separated file that the operator can use to fill in
        concentration measurements from the Qubit. When all data
        has been filled in, the file can be uploaded to BASE and
        the concentration values are imported as annotations.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.QubitSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="FlowCellSampleSheetExporter">
    <about>
      <name>Flow cell sample sheet exporter</name>
      <description>
        Plug-in for exporting information about libraries used in a flow cell.
        The generated tab-separated text file used used by analysis software
        to pick up data from the sequencing.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <extension
    id="net.sf.basedb.reggie"
    extends="net.sf.basedb.clients.web.menu.extensions"
    >
    <index>10</index>
    <about>
      <name>Reggie</name>
      <description>
        Menu entry for accessing reggie-specific operations.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
      </factory-class>
      <parameters>
        <title>Reggie</title>
        <tooltip>Access reggie operations</tooltip>
        <onClick>Menu.openUrl('$HOME$/index.jsp?ID='+getSessionId())</onClick>
        <icon>/images/padding.gif</icon>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.toolbar.case-summary"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
    </extends>
    <about>
      <name>Case summary</name>
      <description>
        Adds a button to the toolbar of sample and extracts pages
        that opens the 'case summary' for the case that the current
        item is part of. Works for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.list-column"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
    </extends>
    <index>2</index>
    <about>
      <name>Reggie column</name>
      <description>
        Add a column to the list page of samples, extract and bioplates
        for including some reggie-specific links.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
      </factory-class>
    </action-factory>
  </extension>
  
  
  <extension
    id="net.sf.basedb.reggie.overview.case-summary"
    extends="net.sf.basedb.clients.web.overview.info-details"
    >
    <index>1</index>
    <about>
      <name>Case overview</name>
      <description>
        Adds a section to the information pane in the "Item overview"
        functionality that display a link to the "Case summary" 
        function in Reggie for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
      </factory-class>
      <parameters>
        <id>reggie.case-summary</id>
        <title>Reggie</title>
        <include>~/reports/case_summary_hook.jsp</include>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.toolbar.histology-score"
    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
    >
    <about>
      <name>Histology score</name>
      <description>
        Adds a button to the toolbar of paraffin blocks and
        HE stain bioplates that start the 'histology scoring wizard'.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
      </factory-class>
    </action-factory>
  </extension>
  
</extensions>