Mercurial > repos > nathandunn > biolinkmonarchinitiative

changeset 2:88e1bd76b069 draft

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planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
author nathandunn
date Thu, 22 Jun 2017 15:28:43 -0400
parents 8fdad43e4250
children d40860663861
files associations.xml bioentity-associations.xml bulk-operations.xml disease-associations.xml gene-associations.xml genotype-associations.xml get-object.xml macros.xml phenotype-gene-associations.xml search-operations.xml substance-associations.xml test-data/diseases-for-genotype.json test-data/genes-for-genotype.json variant-associations.xml
diffstat 14 files changed, 113 insertions(+), 176 deletions(-) [+]
line wrap: on
line diff
--- a/associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,17 +1,17 @@
 <tool id="monarch-associations" name="Associations" version="0.1.0">
-    <requirements/>
-    <stdio>
-        <exit_code range="1:"/>
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="frontmatter" />
     <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' > $output
+        curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$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' > $output
+        curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$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' > $output
+        curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$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' > $output
+        curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
 	#end if
 	]]></command>
     <inputs>
@@ -25,9 +25,7 @@
         </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="subject" value="NCBIGene:84570"/>
@@ -51,12 +49,6 @@
             <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>
+    <expand macro="citations" />
 </tool>
 
--- a/bioentity-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/bioentity-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,30 +1,22 @@
 <tool id="monarch-bioentity-associations" name="Bioentity Associations" 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/bioentity/$input/associations/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/$input/associations/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Bioentity ID (e.g. ZFIN:ZDB-ALT-010427-8)" />
 		<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="ZFIN:ZDB-ALT-010427-8"/>
 			<output name="output" file="associations-for-variant.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>
 
--- 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>
 
--- a/disease-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/disease-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-disease-associations" name="Disease Associations" 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/bioentity/disease/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/disease/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 	    <param  name="input" type="text" format="txt" multiple="false" label="Disease  (e.g. OMIM:605543, DOID:678)" />
@@ -15,9 +15,7 @@
 		</param>
 		<param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
     </inputs>
-    <outputs>
-	        <data name="output" format="json" />
-    </outputs>
+	<expand macro="outputs" />
 	 <tests>
 		 <test>
 			 <param name="input" value="OMIM:605543"/>
@@ -35,11 +33,5 @@
 			 <output name="output" file="phenotypes-for-disease.json"/>
 		 </test>
 	 </tests>
-    <help><![CDATA[
-        Pulls data from Monarch Initiative BioLink API web services as JSON.
-		https://api.monarchinitiative.org/api/
-    ]]></help>
-	<citations>
-		<citation type="doi">doi:10.5281/zenodo.56412</citation>
-    </citations>
+	<expand macro="citations" />
 </tool>
--- a/gene-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/gene-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="monarch-genotype-associations" name="Genotype Associations" version="0.1.0">
-    <requirements/>
-    <stdio>
-        <exit_code range="1:"/>
-    </stdio>
+<tool id="monarch-gene-associations" name="Gene Associations" version="0.1.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="frontmatter" />
     <command><![CDATA[
-curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/gene/$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' > $output
 	]]></command>
     <inputs>
         <param name="input" type="text" format="txt" multiple="false" label="Gene"/>
@@ -17,9 +17,7 @@
         </param>
         <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
     </inputs>
-    <outputs>
-        <data name="output" format="json"/>
-    </outputs>
+    <expand macro="outputs" />
     <tests>
         <test>
             <param name="input" value="NCBIGene:4750"/>
@@ -47,11 +45,5 @@
             <output name="output" file="phenotypes-for-gene.json"/>
         </test>
     </tests>
-    <help><![CDATA[
-        Pulls data from Monarch Initiative BioLink API web services as JSON.
-		https://api.monarchinitiative.org/api/
-    ]]></help>
-    <citations>
-        <citation type="doi">doi:10.5281/zenodo.56412</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
--- a/genotype-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/genotype-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,13 +1,13 @@
 <tool id="monarch-genotype-associations" name="Genotype Associations" version="0.1.0">
-    <requirements/>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="frontmatter" />
 	<command><![CDATA[
-curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/genotype/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/genotype/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
-	    <param  name="input" type="text" format="txt" multiple="false" label="Genotype (e.g. ZFIN:ZDB-FISH-150901-4286)" />
+	    <param  name="input" type="text" format="txt" multiple="false" label="Genotype (e.g. dbSNPIndividual:12141)" />
 		<param  name="association" type="select" multiple="false" display="radio" label="Type">
 			<option value="diseases">Diseases </option>
 			<option value="genes">Genes</option>
@@ -16,36 +16,28 @@
 		</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="ZFIN:ZDB-FISH-150901-4286"/>
+			 <param name="input" value="dbSNPIndividual:12141"/>
 			 <param name="association" value="diseases"/>
 			 <output name="output" file="diseases-for-genotype.json"/>
 		 </test>
          <test>
-             <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
+             <param name="input" value="dbSNPIndividual:12141"/>
              <param name="association" value="genes"/>
              <output name="output" file="genes-for-genotype.json"/>
          </test>
          <test>
-             <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
+             <param name="input" value="dbSNPIndividual:12141"/>
              <param name="association" value="genotypes"/>
              <output name="output" file="genotypes-for-genotype.json"/>
          </test>
          <test>
-             <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
+             <param name="input" value="dbSNPIndividual:12141"/>
              <param name="association" value="phenotypes"/>
              <output name="output" file="phenotypes-for-genotype.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>
--- a/get-object.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/get-object.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-get-object" name="Get Object" 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/bioentity/$type$input$associations?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/$type$input$associations?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Object ID" />
@@ -19,9 +19,7 @@
 		</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="OMIM:605543"/>
@@ -45,12 +43,6 @@
 			<output name="output" file="bioentity-object-for-genotype.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>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -0,0 +1,25 @@
+<macros>
+    <xml name="frontmatter">
+        <requirements>
+        </requirements>
+        <stdio>
+            <exit_code range="1:"/>
+        </stdio>
+        <yield/>
+    </xml>
+    <xml name="citations">
+        <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.815635</citation>
+        </citations>
+        <yield/>
+    </xml>
+    <xml name="outputs">
+        <outputs>
+            <data name="output" format="json"/>
+        </outputs>
+    </xml>
+</macros>
--- a/phenotype-gene-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/phenotype-gene-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,19 +1,17 @@
 <tool id="monarch-phenotype-gene-associations" name="Phenotype Gene Associations" 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/bioentity/phenotype/$input/gene/$taxid/ids?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/phenotype/$input/gene/$taxid/ids?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Phenotype ID (e.g. MP:0001569)" />
 		<param  name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" />
 		<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="MP:0001569"/>
@@ -21,12 +19,6 @@
 			<output name="output" file="phenotype-for-phenotype-and-taxon.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>
 
--- a/search-operations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/search-operations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,18 +1,16 @@
 <tool id="monarch-search-operations" name="Search 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/search/entity/$input?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/search/entity/$input?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Search Term (e.g. shh, parkinson, femur)" />
 		<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="ssh"/>
@@ -27,12 +25,6 @@
 			<output name="output" file="femur-search-term.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>
 
--- a/substance-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/substance-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-substance-associations" name="Substance Associations" 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/bioentity/substance/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/substance/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Substance (e.g. CHEBI:40036)" />
@@ -15,9 +15,7 @@
 		</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="CHEBI:40036"/>
@@ -36,12 +34,6 @@
 			<!--<output name="output" file="treats-for-substance.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>
 
--- a/test-data/diseases-for-genotype.json	Wed Jun 21 19:00:33 2017 -0400
+++ b/test-data/diseases-for-genotype.json	Thu Jun 22 15:28:43 2017 -0400
@@ -1,1 +1,1 @@
-{"associations": [], "compact_associations": null, "objects": [], "start": null, "numFound": null, "facet_pivot": null, "facet_counts": {"subject_taxon_label": {}, "object_closure": {}}}
+{"associations": [{"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": null, "id": null}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "Breast-Ovarian Cancer, Familial, Susceptibility To, 1", "deprecated": null, "id": "OMIM:604370", "description": null, "consider": null}, "id": "f29a7b3f-b587-4133-9459-5a51a0a07097", "type": null, "evidence_graph": {"nodes": [{"lbl": "BRCA1(ARG1443TER) [GM14637]", "id": "dbSNPIndividual:12141"}, {"lbl": null, "id": "MONARCH:60c9082f6214355293ebe52575d8952c8c61cc7e"}, {"lbl": "affected female proband with Breast cancer information core (bic) brca1/brca2 mutation panel dna samples", "id": ":.well-known/genid/person-GM14637"}, {"lbl": "Breast-Ovarian Cancer, Familial, Susceptibility To, 1", "id": "OMIM:604370"}], "edges": [{"sub": ":.well-known/genid/person-GM14637", "pred": "RO:0002200", "obj": "OMIM:604370"}, {"sub": ":.well-known/genid/person-GM14637", "pred": "GENO:0000222", "obj": "dbSNPIndividual:12141"}, {"sub": "MONARCH:60c9082f6214355293ebe52575d8952c8c61cc7e", "pred": "OBAN:association_has_object", "obj": "OMIM:604370"}, {"sub": "MONARCH:60c9082f6214355293ebe52575d8952c8c61cc7e", "pred": "OBAN:association_has_subject", "obj": ":.well-known/genid/person-GM14637"}]}, "subject": {"xrefs": null, "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "BRCA1(ARG1443TER) [GM14637]", "deprecated": null, "id": "dbSNPIndividual:12141", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/coriell.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "has phenotype", "deprecated": null, "id": "RO:0002200", "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}], "compact_associations": null, "objects": ["OMIM:604370"], "start": null, "numFound": null, "facet_pivot": null, "facet_counts": {"subject_taxon_label": {"Homo sapiens": 1}, "object_closure": {"BFO:0000020": 1, "DOID:162": 1, "DOID:229": 1, "DOID:0050736": 1, "DOID:16": 1, "DOID:193": 1, "DOID:0050739": 1, "DOID:120": 1, "DOID:0050686": 1, "BFO:0000016": 1, "DOID:14566": 1, "BFO:0000002": 1, "DOID:15": 1, "DOID:0060118": 1, "DOID:0050177": 1, "DC:0000638": 1, "DOID:28": 1, "DOID:1100": 1, "BFO:0000001": 1, "DOID:1612": 1, "DOID:2394": 1, "DOID:37": 1, "BFO:0000017": 1, "DOID:2277": 1, "DOID:3463": 1}}}
--- a/test-data/genes-for-genotype.json	Wed Jun 21 19:00:33 2017 -0400
+++ b/test-data/genes-for-genotype.json	Thu Jun 22 15:28:43 2017 -0400
@@ -1,1 +1,1 @@
-{"associations": [{"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "atp13a2", "deprecated": null, "id": "ZFIN:ZDB-GENE-061215-126", "description": null, "consider": null}, "id": "5d0e62c7-24fa-4116-b978-d71148e20a23", "type": null, "evidence_graph": {"nodes": [{"lbl": "AB; atp13a2<MO1-atp13a2>", "id": "ZFIN:ZDB-FISH-150901-4286"}, {"lbl": "atp13a2", "id": "ZFIN:ZDB-GENE-061215-126"}, {"lbl": "atp13a2<MO1-atp13a2>", "id": ":.well-known/genid/ZDB-GENE-061215-126-ZDB-MRPHLNO-130130-3"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-061215-126-ZDB-MRPHLNO-130130-3", "pred": "GENO:0000443", "obj": "ZFIN:ZDB-GENE-061215-126"}, {"sub": "ZFIN:ZDB-FISH-150901-4286", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-061215-126-ZDB-MRPHLNO-130130-3"}]}, "subject": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "AB; atp13a2<MO1-atp13a2>", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-4286", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl", "http://data.monarchinitiative.org/ttl/go.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}], "compact_associations": null, "objects": ["ZFIN:ZDB-GENE-061215-126"], "start": null, "numFound": null, "facet_pivot": null, "facet_counts": {"subject_taxon_label": {"Danio rerio": 1}, "object_closure": {"SO:0001411": 1, "ZFIN:ZDB-GENE-061215-126": 1, "BFO:0000031": 1, "owl:Thing": 1, "GENO:0000014": 1, "ENSEMBL:ENSDARG00000061890": 1, "SO:0000110": 1, "SO:0000001": 1, "GENO:0000701": 1, "SO:0000704": 1, "SO:0001217": 1, "NCBIGene:568666": 1, "BFO:0000002": 1, "BFO:0000001": 1}}}
+{"associations": [{"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "BRCA1", "deprecated": null, "id": "NCBIGene:672", "description": null, "consider": null}, "id": "32abb1b1-8213-4205-ab6a-bfd96bac4c03", "type": null, "evidence_graph": {"nodes": [{"lbl": "BRCA1(ARG1443TER) [GM14637]", "id": "dbSNPIndividual:12141"}, {"lbl": "BRCA1, ARG1443TER", "id": "OMIM:113705.0016"}, {"lbl": "BRCA1(ARG1443TER)", "id": ":.well-known/genid/113705.0016"}, {"lbl": "BRCA1", "id": "NCBIGene:672"}], "edges": [{"sub": "dbSNPIndividual:12141", "pred": "GENO:0000382", "obj": ":.well-known/genid/113705.0016"}, {"sub": ":.well-known/genid/113705.0016", "pred": "GENO:0000382", "obj": "OMIM:113705.0016"}, {"sub": "OMIM:113705.0016", "pred": "GENO:0000408", "obj": "NCBIGene:672"}, {"sub": "OMIM:113705.0016", "pred": "GENO:0000408", "obj": "NCBIGene:672"}]}, "subject": {"xrefs": null, "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "BRCA1(ARG1443TER) [GM14637]", "deprecated": null, "id": "dbSNPIndividual:12141", "description": null, "consider": null}, "provided_by": ["https://data.monarchinitiative.org/ttl/omim.ttl", "http://data.monarchinitiative.org/ttl/coriell.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}], "compact_associations": null, "objects": ["NCBIGene:672"], "start": null, "numFound": null, "facet_pivot": null, "facet_counts": {"subject_taxon_label": {"Homo sapiens": 1}, "object_closure": {"OMIM:113705": 1, "Orphanet:119068": 1, "SO:0000001": 1, "owl:Thing": 1, "GENO:0000014": 1, "SO:0000110": 1, "BFO:0000001": 1, "SO:0001411": 1, "BFO:0000002": 1, "NCBIGene:672": 1, "SO:0000704": 1, "HGNC:1100": 1, "SO:0001217": 1, "GENO:0000701": 1, "KEGG-hsa:672": 1, "BFO:0000031": 1, "ENSEMBL:ENSG00000012048": 1}}}
--- a/variant-associations.xml	Wed Jun 21 19:00:33 2017 -0400
+++ b/variant-associations.xml	Thu Jun 22 15:28:43 2017 -0400
@@ -1,10 +1,10 @@
 <tool id="monarch-variant-associations" name="Variant Associations" 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/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
 	]]></command>
 	<inputs>
 		<param  name="input" type="text" format="txt" multiple="false" label="Variant (e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783)" />
@@ -15,9 +15,7 @@
 		</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="ZFIN:ZDB-ALT-010427-8"/>
@@ -35,12 +33,6 @@
 			<output name="output" file="phenotypes-for-variant.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>