annotate variant-associations.xml @ 0:4f6fba8332ec draft

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

<tool id="monarch-variant-associations" name="Variant 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/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>
	<outputs>
		<data name="output" format="json" />
	</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>
	<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>