Add customtrack datatype. This is a skeleton class for now, allows viewing at ucsc and formatted

peeking.

lib/galaxy/datatypes/__init__.py

@@ -23,7 +23,8 @@ datatypes_by_extension = {
     'gmaj.zip' : images.Gmaj(),
     'laj'      : images.Laj(),
     'lav'      : sequence.Lav(),
-    'html'     : images.Html()
+    'html'     : images.Html(),
+    'customtrack' : interval.CustomTrack()
 }
 
 def get_datatype_by_extension( ext ):

lib/galaxy/datatypes/interval.py

@@ -236,6 +236,22 @@ class Gff( Tabular ):
     def make_html_table(self, data):
         return Tabular.make_html_table(self, data, skipchar='#')
 
+#Extend Tabular type, since interval tools will fail on track def line (we should fix this)
+#This is a skeleton class for now, allows viewing at ucsc and formatted peeking.
+class CustomTrack ( Tabular ):
+    """UCSC CustomTrack"""
+    def __init__(self, id=None):
+        data.Text.__init__(self, id=id)
+    
+    def make_html_table(self, dataset):
+        return Tabular.make_html_table(self, dataset, skipchar='track')
+    
+    def bed_viewport( self, dataset ):
+        return "." #Not ideal solution, will cause genome browser to give warning
+    
+    def as_bedfile( self, dataset ):
+        return dataset.file_name
+
 if __name__ == '__main__':
     import doctest, sys
     doctest.testmod(sys.modules[__name__])        

lib/galaxy/interfaces/root.py

@@ -117,7 +117,7 @@ class Universe(common.Root):
         """Returns a bed file"""
         data = self.app.model.Dataset.get( id )
         if data:
-            if isinstance(data.datatype, datatypes.interval.Interval):
+            if isinstance(data.datatype, datatypes.interval.Interval) or isinstance(data.datatype, datatypes.interval.CustomTrack):
                 mime = data.get_mime()
                 trans.response.set_content_type(mime)
                 file_name = data.as_bedfile()

lib/galaxy/util/__init__.py

@@ -74,7 +74,7 @@ text_types = sets.Set([
     'regions', 'simple', 'score', 'text', 'msf', 'selex', 'tagseq', 'embl', 'srspair', 'staden', 
     'strider', 'xbed', 'markx10', 'pair', 'markx1', 'markx0', 'markx3', 'markx2', 'jackknifer', 
     'ncbi', 'mega', 'fa', 'feattable', 'phylip', 'diffseq', 'bed', 'srs', 'jackknifernon', 'swiss', 
-    'phylipnon', 'nexusnon', 'nametable', 'xml', 'interval', 'tabular', 'maf','axt', 'lav', 'laj'
+    'phylipnon', 'nexusnon', 'nametable', 'xml', 'interval', 'tabular', 'maf','axt', 'lav', 'laj', 'customtrack'
 ])     
 
 def parse_xml(fname):

templates/history.tmpl

@@ -203,7 +203,7 @@ main();">
                     #if $data.ext in [ "bed", "interval", "tabular", "txt", "text", "axt", "maf", "fasta", "gff", "gmaj.zip" ]:
                          <a href="display?id=$data.id&tofile=yes&toext=$data.ext" target="_blank">save</a>
                     #end if
-                    #if $data.ext in ["bed", "interval" ]:
+                    #if $data.ext in ["bed", "interval", "customtrack" ]:
                       #set $value = $data.bed_viewport()
                       #if $value
                          | display at UCSC 

tools/data_source/ucsc_tablebrowser_code.py

@@ -3,9 +3,9 @@ from galaxy import datatypes
 
 def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
-    outputType = param_dict.get( 'hgta_outputType', "interval" ) #assume all data is interval, we will fix later if not the case
-    #list for converting ucsc to galaxy exts, if not in here, use raw reported value
-    outputType_to_ext = {'wigData':'wig','tab':'interval','hyperlinks':'html','sequence':'fasta'}
+    outputType = param_dict.get( 'hgta_outputType', "interval" ).lower() #assume all data is interval, we will fix later if not the case
+    #list for converting ucsc to galaxy exts, if not in following dictionary, use provided datatype
+    outputType_to_ext = {'wigdata':'wig','tab':'interval','hyperlinks':'html','sequence':'fasta'}
     items = out_data.items()
     description = param_dict.get('hgta_regionType',"")
     organism = param_dict.get('org',"unkown species")