From 805338420063c86eda5fe13c566b7eb8c2a650b7 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 5 Dec 2013 14:51:06 -0800
Subject: [PATCH] Update for UCSC's validate manifest 1.7

---
 htsworkflow/templates/manifest.txt             | 5 +++--
 htsworkflow/templates/trackhub_manifest.sparql | 5 ++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/htsworkflow/templates/manifest.txt b/htsworkflow/templates/manifest.txt
index c81259c..21c8a47 100644
--- a/htsworkflow/templates/manifest.txt
+++ b/htsworkflow/templates/manifest.txt
@@ -1,2 +1,3 @@
-#file_name	format	output_type	experiment	replicate	enriched_in	ucsc_db	replaces	replace_reason{% for r in files %}
-{{ r.relative_path }}	{{ r.file_format }}	{{ r.output_type }}	{{ r.dataset_id }}	{{ r.replicate }}	{{ r.enriched_in }}	{{ r.ucsc_db }}	{{ r.replaces_accession|default_if_none:"" }}	{{ r.replace_reason|default_if_none:"" }}{% endfor %}
+#version 1.7
+#file_name	format	output_type	experiment	replicate	enriched_in	ucsc_db	paired_end	technical_replicate{% for r in files %}
+{{ r.relative_path }}	{{ r.file_format }}	{{ r.output_type }}	{{ r.dataset_id }}	{{ r.replicate }}	{{ r.enriched_in }}	{{ r.ucsc_db }}	{{ r.paired_end|default_if_none:"n/a" }}	{{ r.technical_replicate|default_if_none:"n/a"}}{% endfor %}
diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
index cb5c4fd..36e57fa 100644
--- 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 ?replaces_accession ?replace_reason
+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 ;
@@ -23,6 +23,9 @@ WHERE {
 
   ?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;
-- 
2.30.2