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

planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty

<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>