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

planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e

<tool id="monarch-gene-associations" name="Gene 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/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>
    <expand macro="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>
    <expand macro="citations" />
</tool>