annotate disease-associations.xml @ 3:d40860663861 draft

planemo upload commit 1a35e82b210719d58263c618f9a67801db26d391

<tool id="monarch-disease-associations" name="Disease Associations" version="0.1.0">
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="frontmatter" />
	<command><![CDATA[
curl --silent -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>
	<expand macro="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>
	<expand macro="citations" />
</tool>