view bulk-operations.xml @ 1:8fdad43e4250 draft

planemo upload commit 2e06360e9b6f5ca9e6d254430878008fa6a57a03

<tool id="monarch-bulk-operations" name="Bulk Operations" 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/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
	]]></command>
    <inputs>
        <param name="taxon" type="text" format="txt" multiple="false" label="Taxon (e.g. NCBITaxon:9606)"/>
        <param name="object_category" type="text" format="txt" multiple="false" label="Object Category (e.g. phenotype, disease)"/>
        <param name="association" type="select" multiple="false" display="radio" label="Type">
            <option value="gene">Gene</option>
            <option value="disease">Disease</option>
            <option value="case">Case</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>
        <!--NOTE: these take way too long to run because fo the large amount of data involved-->
        <!--<test>-->
            <!--<param name="type" value="gene"/>-->
            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
            <!--<param name="rows" value="1"/>-->
            <!--<param name="object_category" value="phenotype"/>-->
            <!--<output name="output" file="gene-mart-for-phenotype.json"/>-->
        <!--</test>-->
        <!--<test>-->
            <!--<param name="type" value="disease"/>-->
            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
            <!--<param name="rows" value="1"/>-->
            <!--<param name="object_category" value="phenotype"/>-->
            <!--<output name="output" file="disease-mart-for-phenotype.json"/>-->
        <!--</test>-->
        <!--<test>-->
            <!--<param name="type" value="case"/>-->
            <!--<param name="taxon" value="NCBITaxon:9606"/>-->
            <!--<param name="rows" value="1"/>-->
            <!--<param name="object_category" value="phenotype"/>-->
            <!--<output name="output" file="case-mart-for-phenotype.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>