add EDAM annotations to interval datatypes.

galaxyproject · Feb 28, 2016 · c75691a · c75691a
1 parent 5c4dcf5
commit c75691a
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
@@ -51,6 +51,7 @@
 class Interval( Tabular ):
     """Tab delimited data containing interval information"""
     edam_format = "format_3475"
+    edam_data = "data_3002"
     file_ext = "interval"
     line_class = "region"
     track_type = "FeatureTrack"
@@ -376,6 +377,7 @@ def interval_dict_dataprovider( self, dataset, **settings ):
 class BedGraph( Interval ):
     """Tab delimited chrom/start/end/datavalue dataset"""
 
+    edam_format = "format_3583"
     file_ext = "bedgraph"
     track_type = "LineTrack"
     data_sources = { "data": "bigwig", "index": "bigwig" }
@@ -583,6 +585,7 @@ def sniff( self, filename ):
 class BedStrict( Bed ):
     """Tab delimited data in strict BED format - no non-standard columns allowed"""
 
+    edam_format = "format_3584"
     file_ext = "bedstrict"
 
     # no user change of datatype allowed
@@ -613,13 +616,14 @@ def sniff( self, filename ):
 
 class Bed6( BedStrict ):
     """Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6"""
-
+    edam_format = "format_3585"
     file_ext = "bed6"
 
 
 class Bed12( BedStrict ):
     """Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12"""
 
+    edam_format = "format_3586"
     file_ext = "bed12"
 
 
@@ -641,6 +645,7 @@ def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, bas
 @dataproviders.decorators.has_dataproviders
 class Gff( Tabular, _RemoteCallMixin ):
     """Tab delimited data in Gff format"""
+    edam_data = "data_1255"
     edam_format = "format_2305"
     file_ext = "gff"
     column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
@@ -1288,6 +1293,7 @@ def wiggle_dict_dataprovider( self, dataset, **settings ):
 
 class CustomTrack ( Tabular ):
     """UCSC CustomTrack"""
+    edam_format = "format_3588"
     file_ext = "customtrack"
 
     def __init__(self, **kwd):
@@ -1440,7 +1446,7 @@ class ENCODEPeak( Interval ):
     This format is used to provide called peaks of signal enrichment based on
     pooled, normalized (interpreted) data. It is a BED6+4 format.
     '''
-
+    edam_format = "format_3612"   
     file_ext = "encodepeak"
     column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ]
     data_sources = { "data": "tabix", "index": "bigwig" }