<tool id="DQuery" name="SAPPARQL" version="1.0.0">
  <description/>
  <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>
  <inputs>
    <param format="ttl" label="Genome Database" multiple="True" name="input" type="data"/>
    <param area="True" label="SPARQL query" name="query" type="text" value="YOUR QUERY HERE">
      <sanitizer>
        <valid initial="string.ascii_letters + string.punctuation + string.whitespace + string.digits"/>
      </sanitizer>
    </param>
    <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"/>
  </inputs>
  <outputs>
    <data format="tsv" label="query.tsv" name="output"/>
  </outputs>
  <help>
===============================
Frequently Asked Queries (FAQs)
===============================

----------------------
Obtain COG information
----------------------

Retrieving COG information from a single or multiple genomes at the same time. ::

   PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
   SELECT ?genome ?label ?letter ?description
   WHERE {
      ?genome a ssb:Genome .
      ?genome ssb:dnaobject ?dna .
      ?dna ssb:feature ?gene .
      ?gene ssb:protein ?protein .
      ?protein ssb:feature ?feature .
      ?feature a ssb:Blast .
      ?feature ssb:evalue ?evalue .
      ?feature ssb:cog ?cog .
      ?cog ssb:cogid ?id .
      ?id ssb:letter ?letter .
      ?id ssb:description ?description .
      ?id ssb:label ?label .
   }
   LIMIT 25

-------------------------------
Obtain GC content + Genome size
-------------------------------

  PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
  SELECT ?genome (?GC/?ATGC AS ?GContent) ?ATGC
  WHERE {
    ?genome a ssb:Genome .
    ?genome ssb:dnaobject ?dna .
    ?dna ssb:sequence ?sequence .
    BIND(STRLEN(REPLACE(?sequence,&quot;[AT]&quot;,&quot;&quot;,&quot;i&quot;)) AS ?GC)
    BIND(STRLEN(?sequence) AS ?ATGC)
  }

  </help>
</tool>