goslimmer.xml

<tool id="goslimmer" name="GOSlimmer" version="1.0.1">
	<description>converts a set of annotation from GO to a given GOSlim version</description>
	<command interpreter="java -jar">GOSlimmer.jar 
--go $go
--slim $slim
--annotation $annotation
--output $output
</command>
    <stdio>
        <exit_code range="1:"  level="fatal"   description="Fatal ERROR exit code greater than 1" />
    </stdio>
	<inputs>
		<param name="go" type="data" format="obo,owl" label="Full Gene Ontology File" help="Full Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
		<param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/>
		<param name="annotation" type="data" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/>
	</inputs>
	<outputs>
		<data name="output" format="tabular" label="Slim Annotations" help="Slim Annotation Table"/>
	</outputs>
	<help>
.. class:: infomark

GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.

It requires:

- -A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
- -A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology).
- -A tabular annotation file in GAF (http://geneontology.org/page/download-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one.

-----

.. class:: infomark

GOSlimmer can also be applied to other pairs of OWL/OBO ontologies where one is a subset of the other and you want to convert annotations from the larger to the smaller one.
	</help>
</tool>