X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Ftemplates%2Ftrackhub_manifest.sparql;fp=htsworkflow%2Ftemplates%2Ftrackhub_manifest.sparql;h=295caa80a2f0b43ccbf16005d5ca015028300415;hp=0000000000000000000000000000000000000000;hb=ad6adfee371e67084e55b94a1e5335263d6fb26b;hpb=6f05ae54b482745afbacc8da7d9cc31f9b067d23

diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
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+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) 
+
+}