Generate manifest files for ENCODE3

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

diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
new file mode 100644 (file)
index 0000000..295caa8
--- /dev/null
+++ b/htsworkflow/templates/trackhub_manifest.sparql
@@ -0,0 +1,32 @@
+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 encode3: <http://jumpgate.caltech.edu/wiki/Encode3#> 
+PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
+
+select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db
+WHERE {
+  <{{submission}}> a submissionOntology:submission ;
+                   submissionOntology:name ?name ;
+                   ucscDaf:has_file ?file .
+
+  ?file ucscDaf:filename ?filename ;
+        ucscDaf:relative_path ?relative_path ;
+        htswlib:library ?library ;
+        a ?fileClass .
+
+  ?fileClass geoSoft:fileTypeLabel ?file_format ;
+             ucscDaf:output_type ?output_type .
+  
+  ?library htswlib:replicate ?replicate ;
+           ucscDaf:enriched_in ?enriched_in;
+           ucscDaf:genome_build ?ucsc_db .
+
+  ?library encode3:dataset_id ?dataset_id .
+  # This is lame! why!!!!
+  # ?library2 encode3:dcc_id ?dcc_library_id .
+  # FILTER (?library = ?library2) 
+
+}