annotate variant-associations.xml @ 2:88e1bd76b069 draft

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

<tool id="monarch-variant-associations" name="Variant 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/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
	]]></command>
	<inputs>
		<param  name="input" type="text" format="txt" multiple="false" label="Variant (e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783)" />
		<param  name="association" type="select" multiple="false" display="radio" label="Type">
			<option value="genes">Genes</option>
			<option value="genotypes">Genotypes</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="ZFIN:ZDB-ALT-010427-8"/>
			<param name="association" value="genes"/>
			<output name="output" file="genes-for-variant.json"/>
		</test>
		<test>
			<param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
			<param name="association" value="genotypes"/>
			<output name="output" file="genotypes-for-variant.json"/>
		</test>
		<test>
			<param name="input" value="ClinVarVariant:65929"/>
			<param name="association" value="phenotypes"/>
			<output name="output" file="phenotypes-for-variant.json"/>
		</test>
	</tests>
	<expand macro="citations" />
</tool>