[[TOC()]]
= XGAP plugins =
New tools can be added as 'plugins' to the XGAP UI as described in http://www.molgenis.org/wiki/MolgenisPlugin.
This typically involves a statement of the form 
{{{
#!xml
<plugin name="MyPlugin" type="java.package.MyPluginCode.java"/>
}}} 

XGAP already has a growing catalog of such plugins. Below these plugins and their status (use, development, planned) are reported. One can find the code plugins in the folder handwritten/java/plugins of XGAP:

== DataWizard - to import/export XGAP data files(in use) ==

[[Image(wizard-small.png)]]

== !MatrixViewer - to view !DataElement objects in the form of a matrix (in use) ==

[[Image(matrixview-small.png)]]

== !RqtlCluster - to run R/QTL calculations on a university computer cluster (in use) ==
Installation of this plugin requires access to a PBS computing cluster.

[[Image(cluster-small.png)]]

== DataArchiver - to import/export xgap investigations as zip files (in use) ==

[[Image(archiver-small.png)]]

== !OntologyBrowser - to browse for ontology terms (in use) ==
Note: performance is still slow as it is based an remote version of the [http://www.ebi.ac.uk/ontology-lookup/ EBI Ontology Lookup Service]

[[Image(olsbrowser-small.png)]]

== !InvestigationOverview - report of all annotations and data in one investigation (in use) ==

[[Image(overview-small.png)]]

== !MatrixRemove - to remove a whole matrix (in use) ==

[[Image(remove-small.png)]]

== !MatrixRplot - minimal visualisations of data matrices (in use) ==

[[Image(rplot-small.png)]]

== KEGGConverter - to convert identifiers using KEGG orthologs (in use) ==

[[Image(kegg-small.png)]]