Mercurial > repos > nathandunn > monarchinitiative
view monarch-variants-for-phenotypes.xml @ 2:3107c58d5c85 draft
planemo upload commit 24de1c1405f1f79859f764da60ba068f2dc88cc6
author | nathandunn |
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date | Mon, 27 Jun 2016 09:39:52 -0400 |
parents | 7ae426ca9054 |
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<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>