Mercurial > repos > nathandunn > biolinkmonarchinitiative
diff genotype-associations.xml @ 0:4f6fba8332ec draft
planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
| author | nathandunn |
|---|---|
| date | Wed, 21 Jun 2017 18:42:56 -0400 |
| parents | |
| children | 88e1bd76b069 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genotype-associations.xml Wed Jun 21 18:42:56 2017 -0400 @@ -0,0 +1,51 @@ +<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/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="association" type="select" multiple="false" display="radio" label="Type"> + <option value="diseases">Diseases </option> + <option value="genes">Genes</option> + <option value="genotypes">Genotypes</option> + <option value="phenotypes">Phenotypes</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="ZFIN:ZDB-FISH-150901-4286"/> + <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="association" value="genes"/> + <output name="output" file="genes-for-genotype.json"/> + </test> + <test> + <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/> + <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="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> +</tool>