comparison sm_api_wrapper.py @ 1:f09a77e52ae5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae

0:0c3f56c85e98

        metavar="<PROJECT TYPE>",
    )
    metas = {
        "outdir": "<OUTPUT DIRECTORY>",
        "target_sequences": "<SEQUENCE[S]>",
        "token": "<TOKEN>",
    }
    parser.add_argument(
        "token",
        help="Authentication token for SWISS-MODEL",
        metavar=metas["token"],
    )
    parser.add_argument(
        "outdir",
        help="Directory to store results in",
        metavar=metas["outdir"],
    )

def _main():
    """Run as script."""
    opts = _parse_args()

    target_sequences = _defastarise_targets(opts.target_sequences)
    # determine class
    whsprr = None
    if opts.project_type.lower() == "automodel":
        whsprr = _AutoModelWhisperer(
            target_sequences, opts.token, project_title=opts.project_title
        )
    elif opts.project_type.lower() == "alignment":
        template_sequence = _defastarise_targets([opts.template_sequence])
        assert len(template_sequence) == 1
        template_sequence = template_sequence[0]
        whsprr = _AlignmentWhisperer(
            target_sequences,
            opts.token,
            template_sequence,
            opts.template_seqres_offset,
            opts.pdb_id,
            opts.auth_asym_id,
            opts.assembly_id,
            project_title=opts.project_title,
        )
    elif opts.project_type.lower() == "usertemplate":
        whsprr = _UserTemplateWhisperer(
            target_sequences,
            opts.token,
            opts.template_file,
            project_title=opts.project_title,
        )
    else:
        raise RuntimeError(

1:f09a77e52ae5

        metavar="<PROJECT TYPE>",
    )
    metas = {
        "outdir": "<OUTPUT DIRECTORY>",
        "target_sequences": "<SEQUENCE[S]>",
    }
    parser.add_argument(
        "outdir",
        help="Directory to store results in",
        metavar=metas["outdir"],
    )

def _main():
    """Run as script."""
    opts = _parse_args()

    token = os.getenv("SWISSMODEL_API_TOKEN")
    if not token:
        print(
            "SWISS-MODEL token is not provided in credentials!",
            file=sys.stderr,
        )
        sys.exit(1)
    target_sequences = _defastarise_targets(opts.target_sequences)
    # determine class
    whsprr = None
    if opts.project_type.lower() == "automodel":
        whsprr = _AutoModelWhisperer(
            target_sequences, token, project_title=opts.project_title
        )
    elif opts.project_type.lower() == "alignment":
        template_sequence = _defastarise_targets([opts.template_sequence])
        assert len(template_sequence) == 1
        template_sequence = template_sequence[0]
        whsprr = _AlignmentWhisperer(
            target_sequences,
            token,
            template_sequence,
            opts.template_seqres_offset,
            opts.pdb_id,
            opts.auth_asym_id,
            opts.assembly_id,
            project_title=opts.project_title,
        )
    elif opts.project_type.lower() == "usertemplate":
        whsprr = _UserTemplateWhisperer(
            target_sequences,
            token,
            opts.template_file,
            project_title=opts.project_title,
        )
    else:
        raise RuntimeError(