comparison decoupler_pathway_inference.py @ 8:9864fd2cc1f0 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 03b4d647e2dd8a333f347d3cfbe3dd5c7b407f61

7:2c5686d627c0

    "--method",
    help="Activity inference method",
    default="mlm",
    required=True,
)
args = parser.parse_args()

# check that either -o or --output is specified
if args.output is None:
    raise ValueError("Please specify either -o or --output")

        "Source, target, and weight columns are not present in the network"
    )


print(type(args.min_n))

if args.method == "mlm":
    dc.run_mlm(
        mat=adata,
        net=network,

8:9864fd2cc1f0

    "--method",
    help="Activity inference method",
    default="mlm",
    required=True,
)

# add activity inference method option
parser.add_argument(
    "-g",
    "--var_gene_symbols_field",
    help="Gene symbols field",
    default=None,
)
args = parser.parse_args()

# check that either -o or --output is specified
if args.output is None:
    raise ValueError("Please specify either -o or --output")

        "Source, target, and weight columns are not present in the network"
    )


print(type(args.min_n))

if args.var_gene_symbols_field and args.var_gene_symbols_field in adata.var.columns:
    # Storing index in a column called 'index_bak'
    adata.var['index_bak'] = adata.var.index
    adata.var.set_index(args.var_gene_symbols_field, inplace=True)


if args.method == "mlm":
    dc.run_mlm(
        mat=adata,
        net=network,