<tool id="dgidb_annotate" name="Annotate with DGI" version="0.1">
    <description>database info</description>
    
    <command interpreter="python">
        dgidb_annotator.py
        #if $expert_curated_only:
            -e
        #end if
        #if $print_all:
            -a
        #end if
        -g $gene_name_col
        $input &gt; $output
    </command>
    <inputs>
        <param name="input" label="Input" type="data" format="tabular"/>
        <param name="expert_curated_only" label="Use Only Expert Curated Results" type="boolean"/>
        <param name="print_all" label="Print All Rows, including those without Annotation" type="boolean"/>
        <param name="gene_name_col" label="Gene Name Column" type="data_column" data_ref="input"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular"/>
    </outputs>

    <stdio>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <tests>
        <test>
            <param name="input" value="in1.tabular"/>
            <param name="expert_curated_only" value="True"/>
            <param name="print_all" value="False"/>
            <param name="gene_name_col" value="1"/>
            <output name="output" file="out1.tabular"/>
        </test>
    </tests>

    <help>
Annotates a tabular dataset with information from the `Drug-Gene Interations database`__

.. __: http://dgidb.genome.wustl.edu/
    </help>
</tool>