diff associations.xml @ 0:4f6fba8332ec draft

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/associations.xml	Wed Jun 21 18:42:56 2017 -0400
@@ -0,0 +1,62 @@
+<tool id="monarch-associations" name="Associations" version="0.1.0">
+    <requirements/>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+	#if $type == 'find'
+        curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output
+	#else if $type == 'from'
+        curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
+	#else if $type == 'to'
+        curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$object?rows=$rows&fetch_objects=true' > $output
+	#else if $type == 'between'
+        curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
+	#end if
+	]]></command>
+    <inputs>
+        <param name="subject" type="text" format="txt" multiple="false" label="Subject"/>
+        <param name="object" type="text" format="txt" multiple="false" label="Object"/>
+        <param name="type" type="select" multiple="false" display="radio" label="Type">
+            <option value="find">Find (subject)</option>
+            <option value="from">From (subject)</option>
+            <option value="to">To (object)</option>
+            <option value="between">Between (subject -> object)</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="subject" value="NCBIGene:84570"/>
+            <param name="type" value="find"/>
+            <output name="output" file="find-associations-for-subject.json"/>
+        </test>
+        <test>
+            <param name="subject" value="NCBIGene:84570"/>
+            <param name="type" value="from"/>
+            <output name="output" file="from-associations-for-subject.json"/>
+        </test>
+        <test>
+            <param name="object" value="MP:0013765"/>
+            <param name="type" value="to"/>
+            <output name="output" file="to-associations-for-object.json"/>
+        </test>
+        <test>
+            <param name="subject" value="MGI:1342287"/>
+            <param name="object" value="MP:0013765"/>
+            <param name="type" value="between"/>
+            <output name="output" file="between-associations.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>
+