Mercurial > repos > nathandunn > biolinkmonarchinitiative
diff genotype-associations.xml @ 2:88e1bd76b069 draft
planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
| author | nathandunn |
|---|---|
| date | Thu, 22 Jun 2017 15:28:43 -0400 |
| parents | 4f6fba8332ec |
| children |
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--- 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>