From 6e90ce1cd98f2bf66b11c3b4143c75170ce69d04 Mon Sep 17 00:00:00 2001 From: Lonneke Scheffer Date: Wed, 8 Nov 2023 18:56:10 +0100 Subject: [PATCH] updates and bugfixes build_dataset_overview_yaml.py --- immuneML/api/galaxy/build_dataset_overview_yaml.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/immuneML/api/galaxy/build_dataset_overview_yaml.py b/immuneML/api/galaxy/build_dataset_overview_yaml.py index 402acdc00..3a9223e28 100644 --- a/immuneML/api/galaxy/build_dataset_overview_yaml.py +++ b/immuneML/api/galaxy/build_dataset_overview_yaml.py @@ -13,7 +13,7 @@ def add_report_with_label(specs, args, report_name, report_key): if args.label_name != "": specs["definitions"]["reports"][f"{report_key}_report"] = {report_name: {"label": args.label_name}} else: - specs["definitions"]["reports"][f"{report_key}_report"] = "VJGeneDistribution" + specs["definitions"]["reports"][f"{report_key}_report"] = report_name specs["instructions"]["my_dataset_generation_instruction"]["analyses"][f"{report_key}_analysis"] = { "dataset": args.dataset_name, "report": f"{report_key}_report"} @@ -61,10 +61,10 @@ def parse_commandline_arguments(args): parser.add_argument("-x", "--existing_dataset", choices=["True", "False"], default="False", help="Whether to use an already existing dataset from the current working directory (use the 'dataset_name' parameter to pass the name).") parser.add_argument("-d", "--dataset_name", default="dataset", help="The name of the dataset to import/export.") - parser.add_argument("-r", "--format", required=True, help="The format of the repertoire/receptor dataset") + parser.add_argument("-r", "--format", help="The format of the repertoire/receptor dataset") parser.add_argument("-m", "--metadata_file", default="", help="The metadata file when using a repertoire dataset. When using a receptor dataset, you may supply an empty string.") - parser.add_argument("-i", "--is_repertoire", choices=["True", "False"], required=True, help="Whether to import a RepertoireDataset") + parser.add_argument("-i", "--is_repertoire", choices=["True", "False"], help="Whether to import a RepertoireDataset") parser.add_argument("-p", "--paired", choices=["True", "False"], default="False", help="When the data is not repertoire data (metadata file = ''), this specifies whether the data is paired (ReceptorDataset) or unpaired (SequenceDataset)") parser.add_argument("-c", "--receptor_chains", choices=["TRA_TRB", "TRG_TRD", "IGH_IGL", "IGH_IGK"], default="TRA_TRB",