diff hubArchiveCreator.py @ 54:4a58094b051e draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty

--- a/hubArchiveCreator.py	Thu May 11 17:27:15 2017 -0400
+++ b/hubArchiveCreator.py	Tue May 16 18:09:00 2017 -0400
@@ -20,6 +20,7 @@
 from BedSimpleRepeats import BedSimpleRepeats
 from BedSpliceJunctions import BedSpliceJunctions
 from Bed import Bed
+from cytoBand import cytoBand
 from BigWig import BigWig
 from util.Fasta import Fasta
 from util.Filters import TraceBackFormatter
@@ -55,6 +56,9 @@
     # Generic Bed (Blastx transformed to bed)
     parser.add_argument('--bed', action='append', help='Bed generic format')
 
+    #cytoBandIdeo
+    parser.add_argument('--cytoBand', action='append', help='Cytoband Track, using cytoBandIdeo.as')
+
     # BigPsl (blat alignment)
     parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
 
@@ -124,6 +128,7 @@
     # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
     array_inputs_bam = args.bam
     array_inputs_bed_generic = args.bed
+    array_inputs_bed_cytoBand = args.cytoBand
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
@@ -152,6 +157,7 @@
     for (inputs, datatype_class) in [
                         (array_inputs_bam, Bam),
                         (array_inputs_bed_generic, Bed),
+                        (array_inputs_bed_cytoBand, cytoBand),
                         (array_inputs_bigwig, BigWig),
                         (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                         (array_inputs_bed_splice_junctions, BedSpliceJunctions),