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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)
  • 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>




Hypertext links




IDs can be linked with a hypertext link. Use the main.additional.annotation.hypertext.links.path global parameter to set a personal additional annotation hypertext links info file which has the following format:




  EnsemblID=http://www.ensembl.org/id/${ID}




For example, a gene named ENSMUST00000013797 in the EnsemblID column will be replaced by a http://www.ensembl.org/id/ENSMUST00000013797 hypertext link.




Default links:

Field Name	Link associated
GI	http://www.ncbi.nlm.nih.gov/nuccore/${ID}
EnsemblID	http://www.ensembl.org/id/${ID}
Ensembl Gene ID	http://www.ensembl.org/id/${ID}
Ensembl Transcript ID	http://www.ensembl.org/id/${ID}
EntrezGeneID	http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=${ID}
EntrezGene ID	http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=${ID}
MGI ID	http://www.informatics.jax.org/marker/${ID}
SGDID	http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=${ID}
Phatr2 Protein HyperLink	http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=Phatr2&tid=${ID}
UCSC ID	https://genome.ucsc.edu/cgi-bin/hgGene?org=&db=hg19&hgg_gene=${ID}
SGD Gene	http://www.yeastgenome.org/locus/${ID}/overview
ZFIN ID	https://zfin.org/${ID}




Note: The following entry in file defined by main.additional.annotation.hypertext.links.path global parameter, will prevent to set hypertext links in the associated field of the output.

  EnsemblID=