Mercurial > repos > nathandunn > biolinkmonarchinitiative

diff phenotype-gene-associations.xml @ 0:4f6fba8332ec draft

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planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
author nathandunn
date Wed, 21 Jun 2017 18:42:56 -0400
parents
children 88e1bd76b069
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype-gene-associations.xml	Wed Jun 21 18:42:56 2017 -0400
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+<tool id="monarch-phenotype-gene-associations" name="Phenotype Gene 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/phenotype/$input/gene/$taxid/ids?rows=$rows&fetch_objects=true' > $output
+	]]></command>
+	<inputs>
+		<param  name="input" type="text" format="txt" multiple="false" label="Phenotype ID (e.g. MP:0001569)" />
+		<param  name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" />
+		<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="MP:0001569"/>
+			<param name="taxid" value="NCBITaxon:10090"/>
+			<output name="output" file="phenotype-for-phenotype-and-taxon.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>
+