<tool id="getgo" name="getgo" version="0.1.0">
    <description>downloads gene ontologies for model organisms</description>
    <macros>
        <import>go_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command interpreter="Rscript">
        getgo.r --genome "$genome"
        --gtf "$gtf"
        --gene_id "$gene_id"
        --output "$output"
        --cats "$cats"
    </command>
    <inputs>
        <param name="gtf" label="select GTF file" help="GO annotations for all gene ids in this GTF will be fetched" type="data" format="gtf"/>
        <param help="Needed to retrieve GO annotations for the selected genome" label="Select the genome source" name="genome" size="3" type="select">
            <options from_data_table="go_genomes"></options>
        </param>
        <param help="Needed for GO analysis" label="Select gene identifier format" name="gene_id" type="select">
            <options from_data_table="go_gene_ids"></options>
        </param>
        <param name="cats" help="Select the categories for which you would like to retrieve ontologies" type="select" multiple="true" display="checkboxes">
            <option value="GO:CC">GO:Cellular Components</option>
            <option value="GO:BP">BiologicalProcesses</option>
            <option value="GO:MF">Molecular Function</option>
            <option value="KEGG">KEGG pathway</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" label="GO category mapping" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="gtf" value="in.gtf" ftype="gtf"></param>
            <param name="genome" value="hg38"></param>
            <param name="gene_id" value="ensGene"></param>
            <param name="cats" value="GO:CC,GO:BP,GO:MF"></param>
            <output name="output" file="go_terms.tab"></output>
        </test>
    </tests>
    <help>

        **What it does**

        Returns a tabular file with GO gene categories for all genes present in the input GTF file.


        </help>
    <citations>
        <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
    </citations>
</tool>