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comparison sappDocker/matrix.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="DMatrix" name="MATSPARQL" version="1.0.1">
2 <description/>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:MATRIX</container>
5 </requirements>
6 <command interpreter="docker">java -jar /sparql/target/sparqljava-0.0.1-SNAPSHOT-jar-with-dependencies.jar '$separate' '-rdf' '$input' '-format' 'TURTLE' '-query' '$query' '-output' '$output' &amp;&amp; Rscript $__tool_directory__/matrix.R '$output' '$output' </command>
7 <inputs>
8 <param format="ttl" label="Genome Database" multiple="True" name="input" type="data"/>
9 <param area="True" label="SPARQL query" name="query" type="text" value="YOUR QUERY HERE"/>
10 <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"/>
11 </inputs>
12 <outputs>
13 <data format="tsv" label="matrix.tsv" name="output"/>
14 </outputs>
15 <help>The creation of a matrix from a created SPARQL query. One should use a query that creates 3 columns for the X and Y coordinates and Z for the value.
16
17 A header for a SPARQL query would look like SELECT ?genome ?protein ?value or SELECT ?genome ?domain (COUNT(?domain) AS ?domainC)
18
19 -----------------------------
20 Genome Interpro Matrix
21 -----------------------------
22 The following query results in a matrix of genomes by Pfam accessions ::
23
24 PREFIX biopax:&lt;http://www.biopax.org/release/bp-level3.owl#&gt;
25 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
26 SELECT DISTINCT ?genome ?id (COUNT(?id) AS ?value)
27 WHERE {
28 ?genome a ssb:Genome .
29 ?genome ssb:dnaobject ?dna .
30 ?dna ssb:feature ?feature .
31 ?feature ssb:tool ?tool .
32 ?feature ssb:protein ?protein .
33 ?protein ssb:feature ?domain .
34 ?domain ssb:signature ?signature .
35 ?signature biopax:xref ?xref .
36 ?xref biopax:db 'pfam' .
37 ?xref biopax:id ?id .
38 } GROUP BY ?genome ?id
39
40 -------------------
41 Enzyme based matrix
42 -------------------
43
44 The following query results in a matrix of genomes by EC numbers ::
45
46 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
47 SELECT ?genome ?ec (COUNT(?ec) AS ?ecCount)
48 WHERE {
49 ?gene a ssb:Cds .
50 ?gene ssb:locus_tag ?locus .
51 ?gene ssb:source ?source .
52 ?gene ssb:protein ?protein .
53 ?protein ssb:feature ?feature .
54 {
55 ?feature ssb:kegg ?ec .
56 } UNION {
57 ?feature ssb:ec_number ?ec .
58 }
59 } GROUP BY ?genome ?ec
60
61 **If you require specific questions related to the database that you created feel free to contact us.**
62 </help>
63 </tool>