Mercurial > repos > nathandunn > monarchinitiative
annotate monarch-variants-for-phenotypes.xml @ 5:7648db7c7168 draft
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author | nathandunn |
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date | Wed, 29 Jun 2016 14:15:57 -0400 |
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1 <tool id="monarch-variants-for-phenotypes" name="Pull Variants from Phenotypes" version="0.1.0"> |
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2 <requirements/> |
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3 <stdio> |
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4 <exit_code range="1:" /> |
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5 </stdio> |
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6 <command><![CDATA[ |
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7 #set conditional = "%20" + str($conditional1) + "%20" |
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8 #set prefix = "object_closure:%22" |
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9 #set suffix = "%22" |
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10 #set inputString = "" |
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11 #for inputFile in $input1 |
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12 #set inputs = open(str($inputFile),'r').read().split(",") |
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13 #for input in $inputs |
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14 #if $inputString != "" |
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15 #set inputString = $inputString + $conditional |
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16 #end if |
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17 #set inputString = $inputString + $prefix + str($input).strip(' \t\n\r') + $suffix |
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18 #end for |
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19 #end for |
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20 |
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21 curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22variant%22&facet.field=subject_taxon_label&q=*:*' | tail -n +2 > $output1 |
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22 ]]></command> |
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23 <inputs> |
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24 <param name="input1" type="data" format="tabular" multiple="true" label="Phenotypes" /> |
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25 <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> |
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26 <option value="AND">and</option> |
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27 <option value="OR">or</option> |
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28 </param> |
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29 </inputs> |
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30 <outputs> |
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31 <data name="output1" type="data" format="tabular" /> |
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32 </outputs> |
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33 <tests> |
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34 <test> |
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35 <param name="input1" value="phenotype.tsv"/> |
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36 <param name="conditional1" value="OR"/> |
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37 <output name="output1" file="variants-for-phenotype.tsv"/> |
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38 </test> |
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39 <test> |
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40 <param name="input1" value="2-phenotypes.tsv"/> |
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41 <param name="conditional1" value="AND"/> |
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42 <output name="output1" file="variants-for-phenotypes-intersection.tsv"/> |
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43 </test> |
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44 <test> |
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45 <param name="input1" value="2-phenotypes.tsv"/> |
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46 <param name="conditional1" value="OR"/> |
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47 <output name="output1" file="variants-for-phenotypes-union.tsv"/> |
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48 </test> |
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49 </tests> |
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50 <help><![CDATA[ |
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51 Pulls data from monarch web services as TSV given a disease.. |
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52 |
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53 subject subject_label relation relation_label object object_label evidence evidence_label source is_defined_by qualifier |
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54 ]]></help> |
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55 <citations> |
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56 <citation type="doi">doi:10.5281/zenodo.56412</citation> |
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57 </citations> |
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58 </tool> |