--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sappDocker/sparql.xml	Wed Jun 29 01:36:58 2016 -0400
@@ -0,0 +1,60 @@
+<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>
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