monarch-variants-for-phenotypes.xml

<tool id="monarch-variants-for-phenotypes" name="Pull Variants from Phenotypes" version="0.1.0">
    <requirements/>
    <stdio>
        <exit_code range="1:" />
    </stdio>
	<command><![CDATA[
#set conditional = "%20" + str($conditional1) + "%20"
#set prefix = "object_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://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22variant%22&facet.field=subject_taxon_label&q=*:*' | tail -n +2 > $output1
	]]></command>
	<inputs>
        <param  name="input1" type="data" format="tabular" multiple="true" label="Phenotypes" />
		<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="tabular" />
    </outputs>
	 <tests>
		 <test>
			 <param name="input1" value="phenotype.tsv"/>
			 <param name="conditional1" value="OR"/>
			 <output name="output1" file="variants-for-phenotype.tsv"/>
		 </test>
		 <test>
			 <param name="input1" value="2-phenotypes.tsv"/>
			 <param name="conditional1" value="AND"/>
			 <output name="output1" file="variants-for-phenotypes-intersection.tsv"/>
		 </test>
		 <test>
			 <param name="input1" value="2-phenotypes.tsv"/>
			 <param name="conditional1" value="OR"/>
			 <output name="output1" file="variants-for-phenotypes-union.tsv"/>
		 </test>
	 </tests>
    <help><![CDATA[
        Pulls data from monarch web services as TSV given a disease..

		subject subject_label relation relation_label object object_label evidence evidence_label source is_defined_by qualifier
    ]]></help>
	<citations>
		<citation type="doi">doi:10.5281/zenodo.56412</citation>
    </citations>
</tool>