<tool id="planteome-gene-associations" name="Gene Associations" version="0.1.0">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="frontmatter" />
    <command><![CDATA[
curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output
	]]></command>
    <inputs>
        <param name="input" type="text" format="txt" multiple="false" label="Gene (e.g. MaizeGDB:9024907)"/>
        <param name="association" type="select" multiple="false" display="radio" label="Type">
            <option value="diseases">Diseases</option>
            <option value="function">Function</option>
            <!--<option value="homologs">Homologs</option>-->
            <!--<option value="interactions">Interactions</option>-->
            <option value="phenotypes">Phenotypes</option>
        </param>
        <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
    </inputs>
    <expand macro="outputs" />
    <tests>
        <test>
            <param name="input" value="MaizeGDB:9024907"/>
            <param name="association" value="diseases"/>
            <output name="output" file="diseases-for-gene.json"/>
        </test>
        <test>
            <param name="input" value="MaizeGDB:9024907"/>
            <param name="association" value="function"/>
            <output name="output" file="function-for-gene.json"/>
        </test>
        <!--<test>-->
            <!--<param name="input" value="MaizeGDB:9024907"/>-->
            <!--<param name="association" value="homologs"/>-->
            <!--<output name="output" file="homologs-for-gene.json"/>-->
        <!--</test>-->
        <!--<test>-->
            <!--<param name="input" value="MaizeGDB:9024907"/>-->
            <!--<param name="association" value="interactions"/>-->
            <!--<output name="output" file="interactions-for-gene.json"/>-->
        <!--</test>-->
        <test>
            <param name="input" value="MaizeGDB:9024907"/>
            <param name="association" value="phenotypes"/>
            <output name="output" file="phenotypes-for-gene.json"/>
        </test>
    </tests>
    <expand macro="citations" />
</tool>