Pass additional information to the trackhub.

[htsworkflow.git] / htsworkflow / templates / trackhub_samples.sparql

diff --git a/htsworkflow/templates/trackhub_samples.sparql b/htsworkflow/templates/trackhub_samples.sparql
index 19ce7e1d5d7f32d35b88e961c867095104dbde88..6259fce15d646aba5864e91d23f22823ce233cac 100644 (file)
--- a/htsworkflow/templates/trackhub_samples.sparql
+++ b/htsworkflow/templates/trackhub_samples.sparql
@@ -1,20 +1,26 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 PREFIX htswlib: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
 PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
 PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX trackdb: <http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#>
 PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
 PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
 PREFIX encode3: <http://jumpgate.caltech.edu/wiki/Encode3#>
 
-select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol 
-
+select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol ?file_label ?autoScale ?maxHeightPixels ?visibility
 WHERE {
-  ?trackType geoSoft:fileTypeLabel ?file_type ;
+  ?trackType trackdb:type ?file_type ;
              ucscDaf:output_type ?output_type .
+  OPTIONAL { ?trackType trackdb:autoScale ?autoScale . }
+  OPTIONAL { ?trackType trackdb:maxHeightPixels ?maxHeightPixels . }
+  OPTIONAL { ?trackType trackdb:visibility ?visibility . }
   ?file ucscDaf:filename ?filename ;
         ucscDaf:relative_path ?relative_path ;
         htswlib:library ?library ;
         a ?trackType .
+  OPTIONAL { ?file rdfs:label ?file_label . }
   OPTIONAL { ?library htswlib:library_id ?lab_library_id }
   OPTIONAL { ?library encode3:library_id ?library_id }
   OPTIONAL { ?library htswlib:cell_line ?cell . }