Mercurial > repos > jjkoehorst > sapp
diff sappDocker/matrix.xml @ 31:957156367442 draft
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author | jjkoehorst |
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date | Wed, 29 Jun 2016 01:36:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sappDocker/matrix.xml Wed Jun 29 01:36:58 2016 -0400 @@ -0,0 +1,63 @@ +<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/target/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> \ No newline at end of file