Expression results annotation module

This module allow to add additional annotations to expression files and create files in TSV, ODS or XLSX formats.

IDs can be linked with a hypertext link with ods and xlsx outputs. For more information check the hypertext link subsection.


  • Internal name: expressionresultsannotation
  • Available: Both local and distributed mode

  • Input ports:
    • expressionfile: expression file in TSV format (format: expression_results_tsv)
    • additionalannotation: additional annotation file in TSV format (format: additional_annotation_tsv) (Not required if use.additional.annotation.file is set to false)

  • Output ports:
    • tsvoutput: expression file with additional annotation in TSV format if requested by user in the parameters of the step (format: annotated_expression_results_tsv)
    • odsoutput: expression file with additional annotation in ODS format if requested by user in the parameters of the step (format: annotated_expression_results_tsv)
    • xlsxoutput: expression file with additional annotation in XLSX format if requested by user in the parameters of the step (format: annotated_expression_results_tsv)

  • Mandatory parameter: None

  • Optional parameters:
  • Parameter Type Default value Description
    use.additional.annotation.file boolean true Set if an additional annotation file must be used.
    output.format string tsv One or more format name for the output separated by a comma.

  • Configuration example:
  • <!-- Additional annotation for expression files -->
    <step skip="false">
    	<module>expressionresultsannotation</module>
    	<parameters>
    		<parameter>
    			<name>output.format</name>
    			<value>xlsx,ods</value>
    		</parameter>
    	</parameters>
    </step>