diff bulk-operations.xml @ 2:88e1bd76b069 draft

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

--- a/bulk-operations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/bulk-operations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-bulk-operations" name="Bulk Operations" 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/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
 	]]></command>
     <inputs>
         <param name="taxon" type="text" format="txt" multiple="false" label="Taxon (e.g. NCBITaxon:9606)"/>
@@ -16,9 +16,7 @@
         </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>
         <!--NOTE: these take way too long to run because fo the large amount of data involved-->
         <!--<test>-->
@@ -43,12 +41,6 @@
             <!--<output name="output" file="case-mart-for-phenotype.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>