Mercurial > repos > jjkoehorst > sapp
view matrix.xml @ 35:fa736576c7ed draft
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author | jjkoehorst |
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date | Mon, 04 Jul 2016 10:37:59 -0400 |
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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' && 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:<http://www.biopax.org/release/bp-level3.owl#> PREFIX ssb:<http://csb.wur.nl/genome/> 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:<http://csb.wur.nl/genome/> 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>