diff jbrowse_hub.py @ 12:e1f188b43750 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

--- a/jbrowse_hub.py	Tue Mar 14 14:00:30 2017 -0400
+++ b/jbrowse_hub.py	Tue Mar 14 14:31:36 2017 -0400
@@ -27,8 +27,11 @@
     # Output folder
     parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")
 
-    # GFF3
-    parser.add_argument('--gff3', action='append', help='GFF3 format')
+    # GFF3 structure: gene->transcription->CDS
+    parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS')
+
+    # GFF3 structure: gene->mRNA->CDS
+    parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')
 
     # trfBig simple repeats (BED 4+12)
     parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
@@ -73,7 +76,8 @@
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
-    array_inputs_gff3 = args.gff3
+    array_inputs_gff3_transcript = args.gff3_transcript
+    array_inputs_gff3_mrna = args.gff3_mrna
     array_inputs_gtf = args.gtf
     array_inputs_blastxml = args.blastxml
     if array_inputs_bam:
@@ -84,8 +88,10 @@
         all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
     if array_inputs_bigwig:
         all_datatype_dictionary['bigwig'] = array_inputs_bigwig
-    if array_inputs_gff3:
-        all_datatype_dictionary['gff3'] = array_inputs_gff3
+    if array_inputs_gff3_transcript:
+        all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
+    if array_inputs_gff3_mrna:
+        all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
     if array_inputs_gtf:
         all_datatype_dictionary['gtf'] = array_inputs_gtf
     if array_inputs_blastxml: