Mercurial > repos > yating-l > jbrowse_hub
comparison jbrowse_hub.py @ 28:5580dbf2a31c draft
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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| 27:e025fa070c8d | 28:5580dbf2a31c |
|---|---|
| 42 # tblastn alignment (blastxml) | 42 # tblastn alignment (blastxml) |
| 43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn') | 43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn') |
| 44 | 44 |
| 45 # BAM format | 45 # BAM format |
| 46 parser.add_argument('--bam', action='append', help='BAM format from HISAT') | 46 parser.add_argument('--bam', action='append', help='BAM format from HISAT') |
| 47 # put bam index file at the same directory with bam file | |
| 48 parser.add_argument('--bai', action='append', help='BAM index format from HISAT') | |
| 49 | 47 |
| 50 # BIGWIG format | 48 # BIGWIG format |
| 51 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage') | 49 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage') |
| 52 | 50 |
| 53 # GTF format | 51 # GTF format |
| 71 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies | 69 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies |
| 72 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin') | 70 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin') |
| 73 chrom_size = utils.getChromSizes(reference, tool_directory) | 71 chrom_size = utils.getChromSizes(reference, tool_directory) |
| 74 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks | 72 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks |
| 75 array_inputs_bam = args.bam | 73 array_inputs_bam = args.bam |
| 76 array_inputs_bai = args.bai | |
| 77 array_inputs_bed_simple_repeats = args.bedSimpleRepeats | 74 array_inputs_bed_simple_repeats = args.bedSimpleRepeats |
| 78 array_inputs_bed_splice_junctions = args.bedSpliceJunctions | 75 array_inputs_bed_splice_junctions = args.bedSpliceJunctions |
| 79 array_inputs_bigwig = args.bigwig | 76 array_inputs_bigwig = args.bigwig |
| 80 array_inputs_gff3_transcript = args.gff3_transcript | 77 array_inputs_gff3_transcript = args.gff3_transcript |
| 81 array_inputs_gff3_mrna = args.gff3_mrna | 78 array_inputs_gff3_mrna = args.gff3_mrna |