comparison jbrowse_hub.py @ 60:ed17bb465bde draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 8386544cbce1efb5e9dd1f805a2099b3e214363f-dirty

59:caf649fc310b

    parser.add_argument('--gtf', action='append', help='GTF format from StringTie')

    # Metadata json format
    parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')

    args = parser.parse_args()
    all_datatype_dictionary = dict()
    

    if not args.fasta:

    reference = args.fasta
    genome = 'unknown'
    out_path = 'unknown.html'
    extra_files_path = '.'
    tool_directory = '.'
    if args.genome_name:
        genome = args.genome_name
    if args.out:
        out_path = args.out
    if args.extra_files_path:

                   # metadata = inputs_data[f]
                    #print metadata
                #Convert tracks into gff3 format
                all_tracks.addToRaw(f, datatype)

    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data)
    jbrowseHub.createHub()

"""        
def extractMetadata(array_inputs, inputs_data):
    metadata_dict = {}

60:ed17bb465bde

    parser.add_argument('--gtf', action='append', help='GTF format from StringTie')

    # Metadata json format
    parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')

    #JBrowse host
    parser.add_argument('--jbrowse_host', help="JBrowse Host")

    args = parser.parse_args()
    all_datatype_dictionary = dict()
    

    if not args.fasta:

    reference = args.fasta
    genome = 'unknown'
    out_path = 'unknown.html'
    extra_files_path = '.'
    tool_directory = '.'
    jbrowse_host = args.jbrowse_host
    if args.genome_name:
        genome = args.genome_name
    if args.out:
        out_path = args.out
    if args.extra_files_path:

                   # metadata = inputs_data[f]
                    #print metadata
                #Convert tracks into gff3 format
                all_tracks.addToRaw(f, datatype)

    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data, jbrowse_host)
    jbrowseHub.createHub()

"""        
def extractMetadata(array_inputs, inputs_data):
    metadata_dict = {}