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

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant-associations.xml	Wed Jun 21 18:42:56 2017 -0400
@@ -0,0 +1,46 @@
+<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>
+