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<tool id="goslimmer" name="GOSlimmer" version="1.0.1">
	<description>converts a set of annotation from GO to a given GOSlim version</description>
    <requirements>
	<requirement type="package" version="8.0.112">java-jdk</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal"   description="Fatal ERROR exit code greater than 1" />
    </stdio>
	<command interpreter="java -jar">GOSlimmer.jar 
--go $go
--slim $slim
--annotation $annotation
--output $output
</command>
	<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"/>
	</outputs>
	<tests>
        	<test>
        	    <param name="go" ftype="obo" value="go.obo"/>
        	    <param name="slim" ftype="obo" value="goslim_generic.obo"/>
	            <param name="annotation" ftype="txt" value="Mus_musculus_annotations_biomart_e92.tab"/>
		    <output name="output" ftype="tabular" file="goslim_annotations_mouse.txt" lines_diff="0"/>
        	</test>
	</tests>
	<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>
    <citations>
        <citation type="bibtex">
@misc{githubgoslimmer,
  author = {Faria, Daniel},
  year = {2017},
  title = {GOSlimmer},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/DanFaria/GOSlimmer},
}</citation>
    </citations>
</tool>