diff jbrowse_hub.py @ 50:3e5b6f6a9abe draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty

--- a/jbrowse_hub.py	Wed Mar 29 14:46:23 2017 -0400
+++ b/jbrowse_hub.py	Thu Mar 30 16:03:16 2017 -0400
@@ -27,11 +27,17 @@
     #Tool Directory
     parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools')
 
+    #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')
+    parser.add_argument('--gff3_transcript', action='append', help='GFF3 format for gene prediction, structure: gene->transcription->CDS')
 
     # GFF3 structure: gene->mRNA->CDS
-    parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')
+    parser.add_argument('--gff3_mrna', action='append', help='GFF3 format for gene prediction, structure: gene->mRNA->CDS')
+
+    # generic BED 
+    parser.add_argument('--bed', action='append', help='BED format')
 
     # trfBig simple repeats (BED 4+12)
     parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
@@ -93,9 +99,11 @@
     all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) 
     
     array_inputs_bam = args.bam
+    array_inputs_bed = args.bed
     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
@@ -103,12 +111,16 @@
 
     if array_inputs_bam:
         all_datatype_dictionary['bam'] = array_inputs_bam
+    if array_inputs_bed:
+        all_datatype_dictionary['bed'] = array_inputs_bed
     if array_inputs_bed_simple_repeats:
         all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
     if array_inputs_bed_splice_junctions:
         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: