<tool id="monarch-disease-associations" name="Disease Associations" version="0.1.0">
    <requirements/>
    <stdio>
        <exit_code range="1:" />
    </stdio>
	<command><![CDATA[
curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/disease/$input/$association/?rows=$rows&fetch_objects=true' > $output
	]]></command>
	<inputs>
	    <param  name="input" type="text" format="txt" multiple="false" label="Disease  (e.g. OMIM:605543, DOID:678)" />
		<param  name="association" type="select" multiple="false" display="radio" label="Type">
			<option value="genes">Genes</option>
			<option value="models">Models</option>
			<option value="phenotypes">Phenotypes</option>
		</param>
		<param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
    </inputs>
    <outputs>
	        <data name="output" format="json" />
    </outputs>
	 <tests>
		 <test>
			 <param name="input" value="OMIM:605543"/>
			 <param name="association" value="genes"/>
			 <output name="output" file="genes-for-disease.json"/>
		 </test>
		 <test>
			 <param name="input" value="OMIM:605543"/>
			 <param name="association" value="models"/>
			 <output name="output" file="models-for-disease.json"/>
		 </test>
		 <test>
			 <param name="input" value="OMIM:605543"/>
			 <param name="association" value="phenotypes"/>
			 <output name="output" file="phenotypes-for-disease.json"/>
		 </test>
	 </tests>
    <help><![CDATA[
        Pulls data from Monarch Initiative BioLink API web services as JSON.
		https://api.monarchinitiative.org/api/
    ]]></help>
	<citations>
		<citation type="doi">doi:10.5281/zenodo.56412</citation>
    </citations>
</tool>