diff hubArchiveCreator.py @ 55:ba9997c847dc draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty

--- a/hubArchiveCreator.py	Tue May 16 18:09:00 2017 -0400
+++ b/hubArchiveCreator.py	Wed May 17 13:16:57 2017 -0400
@@ -30,6 +30,7 @@
 from TrackHub import TrackHub
 from bigPsl import bigPsl
 from BedBlastAlignments import BedBlastAlignments
+from BigBed import BigBed
 
 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
 
@@ -74,6 +75,9 @@
     # Psl Management
     parser.add_argument('--psl', action='append', help='Psl format')
 
+    # BigBed Management
+    parser.add_argument('--bigbed', action='append', help='BigBed format')
+
     # TODO: Check if the running directory can have issues if we run the tool outside
     parser.add_argument('-d', '--directory',
                         help='Running tool directory, where to find the templates. Default is running directory')
@@ -137,6 +141,7 @@
     array_inputs_psl = args.psl
     array_inputs_bigpsl = args.bigpsl
     array_inputs_bed_blast_alignments = args.bedBlastAlignments
+    array_inputs_bigbed = args.bigbed
 
     outputFile = args.output
 
@@ -165,7 +170,8 @@
                         (array_inputs_gtf, Gtf),
                         (array_inputs_psl, Psl),
                         (array_inputs_bigpsl, bigPsl),
-                        (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
+                        (array_inputs_bed_blast_alignments, BedBlastAlignments),
+                        (array_inputs_bigbed, BigBed)]:
         if inputs:
             all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))