comparison hubArchiveCreator.py @ 55:ba9997c847dc draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty

54:4a58094b051e

from Gtf import Gtf
from Psl import Psl
from TrackHub import TrackHub
from bigPsl import bigPsl
from BedBlastAlignments import BedBlastAlignments

# TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort


def main(argv):

    # Bam Management
    parser.add_argument('--bam', action='append', help='Bam format')

    # Psl Management
    parser.add_argument('--psl', action='append', help='Psl format')

    # TODO: Check if the running directory can have issues if we run the tool outside
    parser.add_argument('-d', '--directory',
                        help='Running tool directory, where to find the templates. Default is running directory')
    parser.add_argument('-u', '--ucsc_tools_path',

    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf
    array_inputs_psl = args.psl
    array_inputs_bigpsl = args.bigpsl
    array_inputs_bed_blast_alignments = args.bedBlastAlignments

    outputFile = args.output

    json_inputs_data = args.data_json

                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),
                        (array_inputs_psl, Psl),
                        (array_inputs_bigpsl, bigPsl),
                        (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
        if inputs:
            all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))

    # Create Ordered Dictionary to add the tracks in the tool form order
    all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)

55:ba9997c847dc

from Gtf import Gtf
from Psl import Psl
from TrackHub import TrackHub
from bigPsl import bigPsl
from BedBlastAlignments import BedBlastAlignments
from BigBed import BigBed

# TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort


def main(argv):

    # Bam Management
    parser.add_argument('--bam', action='append', help='Bam format')

    # Psl Management
    parser.add_argument('--psl', action='append', help='Psl format')

    # BigBed Management
    parser.add_argument('--bigbed', action='append', help='BigBed format')

    # TODO: Check if the running directory can have issues if we run the tool outside
    parser.add_argument('-d', '--directory',
                        help='Running tool directory, where to find the templates. Default is running directory')
    parser.add_argument('-u', '--ucsc_tools_path',

    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf
    array_inputs_psl = args.psl
    array_inputs_bigpsl = args.bigpsl
    array_inputs_bed_blast_alignments = args.bedBlastAlignments
    array_inputs_bigbed = args.bigbed

    outputFile = args.output

    json_inputs_data = args.data_json

                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),
                        (array_inputs_psl, Psl),
                        (array_inputs_bigpsl, bigPsl),
                        (array_inputs_bed_blast_alignments, BedBlastAlignments),
                        (array_inputs_bigbed, BigBed)]:
        if inputs:
            all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))

    # Create Ordered Dictionary to add the tracks in the tool form order
    all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)