annotate genotype-associations.xml @ 2:88e1bd76b069 draft

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

<tool id="monarch-genotype-associations" name="Genotype Associations" version="0.1.0">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="frontmatter" />
	<command><![CDATA[
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. dbSNPIndividual:12141)" />
		<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>
    <expand macro="outputs" />
	 <tests>
		 <test>
			 <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="dbSNPIndividual:12141"/>
             <param name="association" value="genes"/>
             <output name="output" file="genes-for-genotype.json"/>
         </test>
         <test>
             <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="dbSNPIndividual:12141"/>
             <param name="association" value="phenotypes"/>
             <output name="output" file="phenotypes-for-genotype.json"/>
         </test>
	 </tests>
    <expand macro="citations" />
</tool>