Mercurial > repos > yating-l > jbrowse_hub
changeset 16:f2285f29a6fa draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
| author | yating-l |
|---|---|
| date | Tue, 14 Mar 2017 15:15:54 -0400 |
| parents | 8627394693c6 |
| children | 99d66676570b |
| files | jbrowse_hub.py |
| diffstat | 1 files changed, 4 insertions(+), 1 deletions(-) [+] |
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--- 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: