view matrix.xml @ 35:fa736576c7ed draft

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<tool id="DMatrix" name="MATSPARQL" version="1.0.1">
  <description/>
  <requirements>
    <container type="docker">jjkoehorst/sappdocker:MATRIX</container>
  </requirements>
  <command interpreter="docker">java -jar /sparql/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>
  <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"/>
    <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="matrix.tsv" name="output"/>
  </outputs>
  <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. 

    A header for a SPARQL query would look like SELECT ?genome ?protein ?value or SELECT ?genome ?domain (COUNT(?domain) AS ?domainC)

-----------------------------
Genome Interpro Matrix
-----------------------------
The following query results in a matrix of genomes by Pfam accessions ::

    PREFIX biopax:&lt;http://www.biopax.org/release/bp-level3.owl#&gt;
    PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
    SELECT DISTINCT ?genome ?id (COUNT(?id) AS ?value)
    WHERE { 
      ?genome a ssb:Genome .
      ?genome ssb:dnaobject ?dna .
      ?dna ssb:feature ?feature .
      ?feature ssb:tool ?tool .
      ?feature ssb:protein ?protein .
      ?protein ssb:feature ?domain .
      ?domain ssb:signature ?signature .
      ?signature biopax:xref ?xref .
      ?xref biopax:db 'pfam' .
      ?xref biopax:id ?id .
      } GROUP BY ?genome ?id

-------------------
Enzyme based matrix
-------------------

The following query results in a matrix of genomes by EC numbers ::

   PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
   SELECT  ?genome ?ec (COUNT(?ec) AS ?ecCount)
   WHERE {
        ?gene a ssb:Cds .
        ?gene ssb:locus_tag ?locus .
        ?gene ssb:source ?source .
        ?gene ssb:protein ?protein .
        ?protein ssb:feature ?feature .
        {
            ?feature ssb:kegg ?ec .
        } UNION {
            ?feature ssb:ec_number ?ec .
        }
   } GROUP BY ?genome ?ec

**If you require specific questions related to the database that you created feel free to contact us.**
  </help>
</tool>