diff substance-associations.xml @ 2:88e1bd76b069 draft

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

--- a/substance-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/substance-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-substance-associations" name="Substance Associations" version="0.1.0">
-	<requirements/>
-	<stdio>
-		<exit_code range="1:" />
-	</stdio>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="frontmatter" />
 	<command><![CDATA[
-curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/substance/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/substance/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Substance (e.g. CHEBI:40036)" />
@@ -15,9 +15,7 @@
 		</param>
 		<param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
 	</inputs>
-	<outputs>
-		<data name="output" format="json" />
-	</outputs>
+	<expand macro="outputs" />
 	<tests>
 		<test>
 			<param name="input" value="CHEBI:40036"/>
@@ -36,12 +34,6 @@
 			<!--<output name="output" file="treats-for-substance.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>
+	<expand macro="citations" />
 </tool>