Update for UCSC's validate manifest 1.7

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

diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
index 295caa80a2f0b43ccbf16005d5ca015028300415..36e57fa88fd0aa21f5cfbf0492b1e2e77365c57b 100644 (file)
--- a/htsworkflow/templates/trackhub_manifest.sparql
+++ b/htsworkflow/templates/trackhub_manifest.sparql
@@ -6,7 +6,7 @@ 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
+select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db ?paired_end ?technical_replicate ?replaces ?replace_reason
 WHERE {
   <{{submission}}> a submissionOntology:submission ;
                    submissionOntology:name ?name ;
@@ -17,16 +17,19 @@ WHERE {
         htswlib:library ?library ;
         a ?fileClass .
 
+  OPTIONAL { ?file encode3:replaces ?replaces_accession ;
+                   encode3:replace_reason ?replace_reason .
+  }
+
   ?fileClass geoSoft:fileTypeLabel ?file_format ;
              ucscDaf:output_type ?output_type .
+  OPTIONAL { ?fileClass ucscDaf:paired_end ?paired_end . }
+  OPTIONAL { ?fileClass ucscDaf:technical_replicate ?technical_replicate . }
+
   
   ?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) 
-
 }