Mercurial > repos > yating-l > jbrowse_hub

comparison jbrowse_hub.py @ 16:f2285f29a6fa draft

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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 e1f188b43750
children a4a54b925c73
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15:8627394693c6 16:f2285f29a6fa
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 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') 48 parser.add_argument('--bai', action='append', help='BAM index format from HISAT')
49 49
50 # BIGWIG format 50 # BIGWIG format
51 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage') 51 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
52 52
53 # GTF format 53 # 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 71 #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') 72 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin')
73 chrom_size = utils.getChromSizes(reference, tool_directory) 73 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 74 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 75 array_inputs_bam = args.bam
76 array_inputs_bai = args.bai
76 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 77 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
77 array_inputs_bed_splice_junctions = args.bedSpliceJunctions 78 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
78 array_inputs_bigwig = args.bigwig 79 array_inputs_bigwig = args.bigwig
79 array_inputs_gff3_transcript = args.gff3_transcript 80 array_inputs_gff3_transcript = args.gff3_transcript
80 array_inputs_gff3_mrna = args.gff3_mrna 81 array_inputs_gff3_mrna = args.gff3_mrna
81 array_inputs_gtf = args.gtf 82 array_inputs_gtf = args.gtf
82 array_inputs_blastxml = args.blastxml 83 array_inputs_blastxml = args.blastxml
83 if array_inputs_bam: 84 if array_inputs_bam:
84 all_datatype_dictionary['bam'] = array_inputs_bam 85 all_datatype_dictionary['bam'] = array_inputs_bam
86 if array_inputs_bai:
87 all_datatype_dictionary['bai'] = array_inputs_bai
85 if array_inputs_bed_simple_repeats: 88 if array_inputs_bed_simple_repeats:
86 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats 89 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
87 if array_inputs_bed_splice_junctions: 90 if array_inputs_bed_splice_junctions:
88 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions 91 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
89 if array_inputs_bigwig: 92 if array_inputs_bigwig: