Mercurial > repos > yating-l > jbrowse_hub

diff jbrowse_hub.py @ 28:5580dbf2a31c draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Wed, 15 Mar 2017 11:36:09 -0400
parents a4a54b925c73
children d8049deb0c97
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--- a/jbrowse_hub.py	Wed Mar 15 10:54:24 2017 -0400
+++ b/jbrowse_hub.py	Wed Mar 15 11:36:09 2017 -0400
@@ -44,8 +44,6 @@
 
     # 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') 
 
     # BIGWIG format
     parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
@@ -73,7 +71,6 @@
     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