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1 <tool id="DQuery" name="SAPPARQL" version="1.0.0">
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2 <description/>
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3 <command interpreter="docker">java -jar /sparql/target/sparqljava-0.0.1-SNAPSHOT-jar-with-dependencies.jar '-rdf' '$input' '-format' 'TURTLE' '-query' '$query' '-output' '$output'</command>
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4 <inputs>
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5 <param format="ttl" label="Genome Database" multiple="True" name="input" type="data"/>
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6 <param area="True" label="SPARQL query" name="query" type="text" value="YOUR QUERY HERE">
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7 <sanitizer>
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8 <valid initial="string.ascii_letters + string.punctuation + string.whitespace + string.digits"/>
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9 </sanitizer>
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10 </param>
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11 <param checked="False" falsevalue="" help="Use this option if you run into memory or performance problems. Each genome will be queried independently of each other and therefor advanced comparison SPARQL queries will not work." label="Treath genomes separately" name="separate" truevalue="-separate" type="boolean"/>
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12 </inputs>
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13 <outputs>
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14 <data format="tsv" label="query.tsv" name="output"/>
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15 </outputs>
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16 <help>
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17 ===============================
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18 Frequently Asked Queries (FAQs)
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19 ===============================
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20
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21 ----------------------
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22 Obtain COG information
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23 ----------------------
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24
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25 Retrieving COG information from a single or multiple genomes at the same time. ::
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26
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27 PREFIX ssb:<http://csb.wur.nl/genome/>
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28 SELECT ?genome ?label ?letter ?description
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29 WHERE {
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30 ?genome a ssb:Genome .
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31 ?genome ssb:dnaobject ?dna .
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32 ?dna ssb:feature ?gene .
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33 ?gene ssb:protein ?protein .
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34 ?protein ssb:feature ?feature .
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35 ?feature a ssb:Blast .
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36 ?feature ssb:evalue ?evalue .
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37 ?feature ssb:cog ?cog .
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38 ?cog ssb:cogid ?id .
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39 ?id ssb:letter ?letter .
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40 ?id ssb:description ?description .
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41 ?id ssb:label ?label .
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42 }
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43 LIMIT 25
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44
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45 -------------------------------
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46 Obtain GC content + Genome size
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47 -------------------------------
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48
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49 PREFIX ssb:<http://csb.wur.nl/genome/>
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50 SELECT ?genome (?GC/?ATGC AS ?GContent) ?ATGC
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51 WHERE {
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52 ?genome a ssb:Genome .
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53 ?genome ssb:dnaobject ?dna .
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54 ?dna ssb:sequence ?sequence .
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55 BIND(STRLEN(REPLACE(?sequence,"[AT]","","i")) AS ?GC)
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56 BIND(STRLEN(?sequence) AS ?ATGC)
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57 }
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58
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59 </help>
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60 </tool> |
