Mercurial > repos > yating-l > hubarchivecreator

comparison hubArchiveCreator.py @ 55:ba9997c847dc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
author yating-l
date Wed, 17 May 2017 13:16:57 -0400
parents 4a58094b051e
children 4ca7cbf2d9b8
comparison
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54:4a58094b051e 55:ba9997c847dc
28 from Gtf import Gtf 28 from Gtf import Gtf
29 from Psl import Psl 29 from Psl import Psl
30 from TrackHub import TrackHub 30 from TrackHub import TrackHub
31 from bigPsl import bigPsl 31 from bigPsl import bigPsl
32 from BedBlastAlignments import BedBlastAlignments 32 from BedBlastAlignments import BedBlastAlignments
33 from BigBed import BigBed
33 34
34 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort 35 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
35 36
36 37
37 def main(argv): 38 def main(argv):
71 # Bam Management 72 # Bam Management
72 parser.add_argument('--bam', action='append', help='Bam format') 73 parser.add_argument('--bam', action='append', help='Bam format')
73 74
74 # Psl Management 75 # Psl Management
75 parser.add_argument('--psl', action='append', help='Psl format') 76 parser.add_argument('--psl', action='append', help='Psl format')
77
78 # BigBed Management
79 parser.add_argument('--bigbed', action='append', help='BigBed format')
76 80
77 # TODO: Check if the running directory can have issues if we run the tool outside 81 # TODO: Check if the running directory can have issues if we run the tool outside
78 parser.add_argument('-d', '--directory', 82 parser.add_argument('-d', '--directory',
79 help='Running tool directory, where to find the templates. Default is running directory') 83 help='Running tool directory, where to find the templates. Default is running directory')
80 parser.add_argument('-u', '--ucsc_tools_path', 84 parser.add_argument('-u', '--ucsc_tools_path',
135 array_inputs_gff3 = args.gff3 139 array_inputs_gff3 = args.gff3
136 array_inputs_gtf = args.gtf 140 array_inputs_gtf = args.gtf
137 array_inputs_psl = args.psl 141 array_inputs_psl = args.psl
138 array_inputs_bigpsl = args.bigpsl 142 array_inputs_bigpsl = args.bigpsl
139 array_inputs_bed_blast_alignments = args.bedBlastAlignments 143 array_inputs_bed_blast_alignments = args.bedBlastAlignments
144 array_inputs_bigbed = args.bigbed
140 145
141 outputFile = args.output 146 outputFile = args.output
142 147
143 json_inputs_data = args.data_json 148 json_inputs_data = args.data_json
144 149
163 (array_inputs_bed_splice_junctions, BedSpliceJunctions), 168 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
164 (array_inputs_gff3, Gff3), 169 (array_inputs_gff3, Gff3),
165 (array_inputs_gtf, Gtf), 170 (array_inputs_gtf, Gtf),
166 (array_inputs_psl, Psl), 171 (array_inputs_psl, Psl),
167 (array_inputs_bigpsl, bigPsl), 172 (array_inputs_bigpsl, bigPsl),
168 (array_inputs_bed_blast_alignments, BedBlastAlignments)]: 173 (array_inputs_bed_blast_alignments, BedBlastAlignments),
174 (array_inputs_bigbed, BigBed)]:
169 if inputs: 175 if inputs:
170 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) 176 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
171 177
172 # Create Ordered Dictionary to add the tracks in the tool form order 178 # Create Ordered Dictionary to add the tracks in the tool form order
173 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) 179 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)