comparison hubArchiveCreator.py @ 54:4a58094b051e draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty

53:44059c9e7c02

# Internal dependencies
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
from BedSpliceJunctions import BedSpliceJunctions
from Bed import Bed
from BigWig import BigWig
from util.Fasta import Fasta
from util.Filters import TraceBackFormatter
from Gff3 import Gff3
from Gtf import Gtf

    parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')

    # Generic Bed (Blastx transformed to bed)
    parser.add_argument('--bed', action='append', help='Bed generic format')

    # BigPsl (blat alignment)
    parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')

    # Bed12+12 (tblastn alignment)
    parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')

    # These inputs are populated in the Galaxy Wrapper xml and are in this format:
    # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
    # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
    array_inputs_bam = args.bam
    array_inputs_bed_generic = args.bed
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf

    all_datatype_dictionary = {}

    for (inputs, datatype_class) in [
                        (array_inputs_bam, Bam),
                        (array_inputs_bed_generic, Bed),
                        (array_inputs_bigwig, BigWig),
                        (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),

54:4a58094b051e

# Internal dependencies
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
from BedSpliceJunctions import BedSpliceJunctions
from Bed import Bed
from cytoBand import cytoBand
from BigWig import BigWig
from util.Fasta import Fasta
from util.Filters import TraceBackFormatter
from Gff3 import Gff3
from Gtf import Gtf

    parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')

    # Generic Bed (Blastx transformed to bed)
    parser.add_argument('--bed', action='append', help='Bed generic format')

    #cytoBandIdeo
    parser.add_argument('--cytoBand', action='append', help='Cytoband Track, using cytoBandIdeo.as')

    # BigPsl (blat alignment)
    parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')

    # Bed12+12 (tblastn alignment)
    parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')

    # These inputs are populated in the Galaxy Wrapper xml and are in this format:
    # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
    # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
    array_inputs_bam = args.bam
    array_inputs_bed_generic = args.bed
    array_inputs_bed_cytoBand = args.cytoBand
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf

    all_datatype_dictionary = {}

    for (inputs, datatype_class) in [
                        (array_inputs_bam, Bam),
                        (array_inputs_bed_generic, Bed),
                        (array_inputs_bed_cytoBand, cytoBand),
                        (array_inputs_bigwig, BigWig),
                        (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),