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comparison sappDocker/sparql.xml @ 31:957156367442 draft

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author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
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30:0a947cb25a3d 31:957156367442
1 <tool id="DQuery" name="SAPPARQL" version="1.0.0">
2 <description/>
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>
4 <inputs>
5 <param format="ttl" label="Genome Database" multiple="True" name="input" type="data"/>
6 <param area="True" label="SPARQL query" name="query" type="text" value="YOUR QUERY HERE">
7 <sanitizer>
8 <valid initial="string.ascii_letters + string.punctuation + string.whitespace + string.digits"/>
9 </sanitizer>
10 </param>
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"/>
12 </inputs>
13 <outputs>
14 <data format="tsv" label="query.tsv" name="output"/>
15 </outputs>
16 <help>
17 ===============================
18 Frequently Asked Queries (FAQs)
19 ===============================
20
21 ----------------------
22 Obtain COG information
23 ----------------------
24
25 Retrieving COG information from a single or multiple genomes at the same time. ::
26
27 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
28 SELECT ?genome ?label ?letter ?description
29 WHERE {
30 ?genome a ssb:Genome .
31 ?genome ssb:dnaobject ?dna .
32 ?dna ssb:feature ?gene .
33 ?gene ssb:protein ?protein .
34 ?protein ssb:feature ?feature .
35 ?feature a ssb:Blast .
36 ?feature ssb:evalue ?evalue .
37 ?feature ssb:cog ?cog .
38 ?cog ssb:cogid ?id .
39 ?id ssb:letter ?letter .
40 ?id ssb:description ?description .
41 ?id ssb:label ?label .
42 }
43 LIMIT 25
44
45 -------------------------------
46 Obtain GC content + Genome size
47 -------------------------------
48
49 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
50 SELECT ?genome (?GC/?ATGC AS ?GContent) ?ATGC
51 WHERE {
52 ?genome a ssb:Genome .
53 ?genome ssb:dnaobject ?dna .
54 ?dna ssb:sequence ?sequence .
55 BIND(STRLEN(REPLACE(?sequence,&quot;[AT]&quot;,&quot;&quot;,&quot;i&quot;)) AS ?GC)
56 BIND(STRLEN(?sequence) AS ?ATGC)
57 }
58
59 </help>
60 </tool>