comparison decoupler_pseudobulk.py @ 2:130e25d3ce92 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85a3118a571246d88aaad26733d0c62009cb736b

1:046d8ff974ff

    # Load AnnData object from file
    adata = anndata.read_h5ad(args.adata_file)

    # Merge adata.obs fields specified in args.adata_obs_fields_to_merge
    if args.adata_obs_fields_to_merge:
        fields = args.adata_obs_fields_to_merge.split(",")
        check_fields(fields, adata)
        adata = merge_adata_obs_fields(fields, adata)

    check_fields([args.groupby, args.sample_key], adata)

    factor_fields = None
    if args.factor_fields:

    parser.add_argument("adata_file", type=str, help="Path to the AnnData file")
    parser.add_argument(
        "-m",
        "--adata_obs_fields_to_merge",
        type=str,
        help="Fields in adata.obs to merge, comma separated",
    )
    parser.add_argument(
        "--groupby",
        type=str,
        required=True,

2:130e25d3ce92

    # Load AnnData object from file
    adata = anndata.read_h5ad(args.adata_file)

    # Merge adata.obs fields specified in args.adata_obs_fields_to_merge
    if args.adata_obs_fields_to_merge:
        # first split potential groups by ":" and iterate over them
        for group in args.adata_obs_fields_to_merge.split(":"):
            fields = group.split(",")
            check_fields(fields, adata)
            adata = merge_adata_obs_fields(fields, adata)

    check_fields([args.groupby, args.sample_key], adata)

    factor_fields = None
    if args.factor_fields:

    parser.add_argument("adata_file", type=str, help="Path to the AnnData file")
    parser.add_argument(
        "-m",
        "--adata_obs_fields_to_merge",
        type=str,
        help="Fields in adata.obs to merge, comma separated. You can have more than one set of fields, separated by semi-colon ;",
    )
    parser.add_argument(
        "--groupby",
        type=str,
        required=True,