<tool id="getgo" name="get_gene_categories" version="0.1.0">
    <description>retrieve gene categories for model organisms</description>
    <macros>
        <import>go_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
        Rscript $__tool_directory__/getgo.r
        --package "$package"
        --gene_id "$gene_id"
        --output "$output"
        --cats "$cats"
        ]]>
    </command>
    <inputs>
        <param help="These are bioconductor genome annotation packages." label="Select the genome package" name="package" size="3" type="select">
            <options from_data_table="org_names"></options>
        </param>
        <param help="This option determines which gene identifier format is used for mapping genes to categories in the output file. If you have a list of differentially expressed genes, choose the same format." label="Select gene identifier format" name="gene_id" type="select">
            <options from_data_table="available_identifiers">
                <filter type="param_value" ref="package" column="2"/>
            </options>
        </param>
        <param name="cats" label="Select categories" help="Select a category will return the category and a list of all genes in that category" type="select" multiple="true" display="checkboxes">
            <options from_data_table="available_categories">
                <filter type="param_value" ref="package" column="2"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" label="gene category mapping" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="package" value="org.Hs.eg.db"></param>
            <param name="gene_id" value="ENSEMBL"></param>
            <param name="cats" value="GO2ALLEGS"></param>
            <output name="output" file="go_terms.tab" compare="contains"></output>
        </test>
    </tests>
    <help>

        **What it does**

        This tool uses bioconductor species annotation packages [org.Xx.xx.db] to extract gene category information.
        To do gene {category/set} enrichment analysis, use the output of this tool with the goseq tool.

        </help>
    <citations>
        <citation type="bibtex">@ARTICLE{AnnotationDbi,
        title = {AnnotationDbi: Annotation Database Interface},
        author = {Herve Pages and Marc Carlson and Seth Falcon and Nianhua Li},
        note = {R package version 1.32.3}
        }
        </citation>
    </citations>
</tool>