4.8. augur_from_beast_mcc

Visualize BEAST output with Nextstrain. This workflow converts a BEAST MCC tree (.tree file) into an Auspice v2 json file. See https://nextstrain-augur.readthedocs.io/en/stable/faq/import-beast.html for details.

4.8.1. Inputs

4.8.1.1. Required inputs

augur_from_beast_mcc.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction

augur_from_beast_mcc.beast_mcc_tree
File — Default: None
A maximum clade credibility (MCC) tree (.tree file) that is output from a BEAST run.

4.8.1.2. Other inputs

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augur_from_beast_mcc.augur_import_beast.docker
String — Default: "nextstrain/base:build-20200629T201240Z"
???

augur_from_beast_mcc.augur_import_beast.machine_mem_gb
Int? — Default: None
???

augur_from_beast_mcc.augur_import_beast.most_recent_tip_date
Float? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_delimiter
String? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_format
String? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_regex
String? — Default: None
???

augur_from_beast_mcc.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.description_md
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.docker
String — Default: "nextstrain/base:build-20200629T201240Z"
???

augur_from_beast_mcc.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.sample_metadata
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.title
String? — Default: None
???

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