monarch-phenopackets.xml

<tool id="monarch-phenopackets-for-disease" name="Pull Phenotypes as Phenopackets for Diseases" version="0.1.0">
    <requirements/>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command><![CDATA[
#set conditional = "%20" + str($conditional1) + "%20"
#set prefix = "subject_closure:%22"
#set suffix = "%22"
#set inputString = ""
#for inputFile in $input1
  #set inputs = open(str($inputFile),'r').read().split(",")
  #for input in $inputs
    #if $inputString != ""
      #set inputString = $inputString + $conditional
    #end if
    #set inputString = $inputString + $prefix + str($input).strip(' \t\n\r') + $suffix
  #end for
#end for

curl -s 'https://monarchinitiative.org/phenopacket?q=*:*&fq=($inputString)&sfq=subject_category:%22variant%22&personality=variant_phenotype' > $output1
	]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" multiple="true" label="Variant"/>
        <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional">
            <option value="AND">and</option>
            <option value="OR">or</option>
        </param>
    </inputs>
    <outputs>
        <data name="output1" type="data" format="json"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="phenotype.tsv"/>
            <param name="conditional1" value="OR"/>
            <!--<output name="output1" file="phenotypes-for-variant.json"/>-->
            <output name="output1">
                <assert_contents>
					<has_text text='phenopacket":{"phenotype_profile":[{"entity":"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input1" value="2-phenotypes.tsv"/>
            <param name="conditional1" value="AND"/>
            <!--<output name="output1" file="phenotypes-for-variants-intersection.json"/>-->
            <output name="output1">
                <assert_contents>
                    <has_text text='{"phenopacket":{"phenotype_profile":[{"entity":"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input1" value="2-phenotypes.tsv"/>
            <param name="conditional1" value="OR"/>
            <!--<output name="output1" file="phenotypes-for-variants-union.json"/>-->
            <output name="output1">
                <assert_contents>
                    <has_text text='{"phenopacket":{"phenotype_profile":[{"entity":"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Pulls phenopacket from data from monarch web services from one or more variants.
		https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started
    ]]></help>
    <citations>
        <citation type="doi">doi:10.5281/zenodo.56412</citation>
    </citations>
</tool>