diff gene-associations.xml @ 0:4f6fba8332ec draft

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene-associations.xml	Wed Jun 21 18:42:56 2017 -0400
@@ -0,0 +1,57 @@
+<tool id="monarch-genotype-associations" name="Genotype Associations" 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/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output
+	]]></command>
+    <inputs>
+        <param name="input" type="text" format="txt" multiple="false" label="Gene"/>
+        <param name="association" type="select" multiple="false" display="radio" label="Type">
+            <option value="diseases">Diseases (e.g,. NCBIGene:4750, Orphanet:173505)</option>
+            <option value="function">Function (e.g,. NCBIGene:4750, Orphanet:173505)</option>
+            <option value="homologs">Homologs (e.g,. NCBIGene:4750, Orphanet:173505)</option>
+            <option value="interactions">Interactions (e.g,. NCBIGene:4750, Orphanet:173505)</option>
+            <option value="phenotypes">Phenotypes (e.g,. NCBIGene:4750, Orphanet:173505)</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="input" value="NCBIGene:4750"/>
+            <param name="association" value="diseases"/>
+            <output name="output" file="diseases-for-gene.json"/>
+        </test>
+        <test>
+            <param name="input" value="NCBIGene:4750"/>
+            <param name="association" value="function"/>
+            <output name="output" file="function-for-gene.json"/>
+        </test>
+        <test>
+            <param name="input" value="NCBIGene:4750"/>
+            <param name="association" value="homologs"/>
+            <output name="output" file="homologs-for-gene.json"/>
+        </test>
+        <test>
+            <param name="input" value="NCBIGene:4750"/>
+            <param name="association" value="interactions"/>
+            <output name="output" file="interactions-for-gene.json"/>
+        </test>
+        <test>
+            <param name="input" value="NCBIGene:4750"/>
+            <param name="association" value="phenotypes"/>
+            <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>
+</tool>