# HG changeset patch
# User yating-l
# Date 1489518954 14400
# Node ID f2285f29a6fa58033832c4459f53f310a0dc56a5
# Parent  8627394693c691013cc8289e5b32f7f623e14c6d
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

diff -r 8627394693c6 -r f2285f29a6fa jbrowse_hub.py
--- a/jbrowse_hub.py	Tue Mar 14 14:57:39 2017 -0400
+++ b/jbrowse_hub.py	Tue Mar 14 15:15:54 2017 -0400
@@ -45,7 +45,7 @@
     # BAM format
     parser.add_argument('--bam', action='append', help='BAM format from HISAT')
     # put bam index file at the same directory with bam file
-    # parser.add_argument('--bai', action='append', help='BAM index format from HISAT') 
+    parser.add_argument('--bai', action='append', help='BAM index format from HISAT') 
 
     # BIGWIG format
     parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
@@ -73,6 +73,7 @@
     chrom_size = utils.getChromSizes(reference, tool_directory)
     all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
     array_inputs_bam = args.bam
+    array_inputs_bai = args.bai
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
@@ -82,6 +83,8 @@
     array_inputs_blastxml = args.blastxml
     if array_inputs_bam:
         all_datatype_dictionary['bam'] = array_inputs_bam
+    if array_inputs_bai:
+        all_datatype_dictionary['bai'] = array_inputs_bai
     if array_inputs_bed_simple_repeats:
         all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
     if array_inputs_bed_splice_junctions: