<tool id="goslimmer" name="GOSlimmer" version="1.0.1">
    <description>converts a set of annotation from GO to a given GOSlim version</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0">goslimmer</requirement>
    </requirements>
    <command detect_errors="exit_code">goslimmer 
--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 @ONTOLOGY_URL@)"/>
        <param name="slim" type="data" format="obo,owl" label="GOSlim File" help="Slim Gene Ontology file in OBO or OWL format (see @ONTOLOGY_URL@)"/>
        <param name="annotation" type="data" format="tabular,txt" 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="annotations.tab"/>
            <output name="output" ftype="tabular" file="slim_annotations.tab" 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 @ONTOLOGY_URL@).
- A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
- A tabular annotation file in GAF (@ANNOTATION_URL@) 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>