diff bulk-operations.xml @ 0:4f6fba8332ec draft

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bulk-operations.xml	Wed Jun 21 18:42:56 2017 -0400
@@ -0,0 +1,54 @@
+<tool id="monarch-bulk-operations" name="Bulk Operations" version="0.1.0">
+    <requirements/>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <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
+	]]></command>
+    <inputs>
+        <param name="taxon" type="text" format="txt" multiple="false" label="Taxon (e.g. NCBITaxon:9606)"/>
+        <param name="object_category" type="text" format="txt" multiple="false" label="Object Category (e.g. phenotype, disease)"/>
+        <param name="association" type="select" multiple="false" display="radio" label="Type">
+            <option value="gene">Gene</option>
+            <option value="disease">Disease</option>
+            <option value="case">Case</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>
+        <!--NOTE: these take way too long to run because fo the large amount of data involved-->
+        <!--<test>-->
+            <!--<param name="type" value="gene"/>-->
+            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
+            <!--<param name="rows" value="1"/>-->
+            <!--<param name="object_category" value="phenotype"/>-->
+            <!--<output name="output" file="gene-mart-for-phenotype.json"/>-->
+        <!--</test>-->
+        <!--<test>-->
+            <!--<param name="type" value="disease"/>-->
+            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
+            <!--<param name="rows" value="1"/>-->
+            <!--<param name="object_category" value="phenotype"/>-->
+            <!--<output name="output" file="disease-mart-for-phenotype.json"/>-->
+        <!--</test>-->
+        <!--<test>-->
+            <!--<param name="type" value="case"/>-->
+            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
+            <!--<param name="rows" value="1"/>-->
+            <!--<param name="object_category" value="phenotype"/>-->
+            <!--<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>
+</tool>
+