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

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

--- a/gene-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/gene-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="monarch-genotype-associations" name="Genotype Associations" version="0.1.0">
-    <requirements/>
-    <stdio>
-        <exit_code range="1:"/>
-    </stdio>
+<tool id="monarch-gene-associations" name="Gene Associations" version="0.1.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="frontmatter" />
     <command><![CDATA[
-curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
     <inputs>
         <param name="input" type="text" format="txt" multiple="false" label="Gene"/>
@@ -17,9 +17,7 @@
         </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="NCBIGene:4750"/>
@@ -47,11 +45,5 @@
             <output name="output" file="phenotypes-for-gene.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>