Mercurial > repos > nathandunn > monarchinitiative
view monarch-phenopackets.xml @ 4:4be31c7908af draft
planemo upload commit 9608f0096fcafb3202cde18a424264ad66130a21
author | nathandunn |
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date | Mon, 27 Jun 2016 09:48:53 -0400 |
parents | 7ae426ca9054 |
children | 7648db7c7168 |
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<tool id="monarch-phenotypes-for-disease" name="Pull Diseases from Phenotypes" 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":"ClinVarVariant:217207"'/> </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":"ClinVarVariant:217207"'/> </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":"ClinVarVariant:217207"'/> </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>