Mercurial > repos > nathandunn > biolinkplanteome

diff get-object.xml @ 0:028a3ffc17b4 draft

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planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
author nathandunn
date Fri, 23 Jun 2017 15:04:12 -0400
parents
children 66ece4fd024f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get-object.xml	Fri Jun 23 15:04:12 2017 -0400
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+<tool id="planteome-get-object" name="Get Object" version="0.1.0">
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="frontmatter" />
+	<command><![CDATA[
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/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>
+	<expand macro="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>
+	<expand macro="citations" />
+</tool>
+