Mercurial > repos > nathandunn > biolinkmonarchinitiative

diff get-object.xml @ 0:4f6fba8332ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
author nathandunn
date Wed, 21 Jun 2017 18:42:56 -0400
parents
children 88e1bd76b069
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get-object.xml	Wed Jun 21 18:42:56 2017 -0400
@@ -0,0 +1,56 @@
+<tool id="monarch-get-object" name="Get Object" 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/$type$input$associations?rows=$rows&fetch_objects=true' > $output
+	]]></command>
+	<inputs>
+		<param  name="input" type="text" format="txt" multiple="false" label="Object ID" />
+		<param  name="type" type="select" multiple="false" display="radio" label="Type">
+			<option value="">Any</option>
+			<option value="gene/">Gene (e.g. NCBIGene:84570)</option>
+			<option value="genotype/">Genotype (e.g. ZFIN:ZDB-FISH-150901-6607)</option>
+		</param>
+		<param  name="associations" type="select" multiple="false" display="radio" label="Render Associations">
+			<option value="/associations/">True</option>
+			<option value="" checked="true">False</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="OMIM:605543"/>
+			<param name="type" value=""/>
+			<output name="output" file="bioentity-object-for-disease.json"/>
+		</test>
+		<test>
+			<param name="input" value="OMIM:605543"/>
+			<param name="type" value=""/>
+			<param name="associations" value="/associations/"/>
+			<output name="output" file="bioentity-associations-for-disease.json"/>
+		</test>
+		<test>
+			<param name="input" value="NCBIGene:84570"/>
+			<param name="association" value="gene/"/>
+			<output name="output" file="bioentity-object-for-gene.json"/>
+		</test>
+		<test>
+			<param name="input" value="ZFIN:ZDB-FISH-150901-6607"/>
+			<param name="association" value="genotype/"/>
+			<output name="output" file="bioentity-object-for-genotype.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>
+