4.6. augur_export_only

Convert a newick formatted phylogenetic tree with other config settings and node values into a json suitable for auspice visualization. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/export.html

4.6.1. Inputs

4.6.1.1. Required inputs

augur_export_only.export_auspice_json.auspice_config
File — Default: None
???

augur_export_only.export_auspice_json.node_data_jsons
Array[File] — Default: None
???

augur_export_only.export_auspice_json.tree
File — Default: None
???

4.6.1.2. Other inputs

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

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

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

augur_export_only.export_auspice_json.disk_size
Int — Default: 300
???

augur_export_only.export_auspice_json.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

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

augur_export_only.export_auspice_json.include_root_sequence
Boolean — Default: true
???

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

augur_export_only.export_auspice_json.machine_mem_gb
Int — Default: 64
???

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

augur_export_only.export_auspice_json.out_basename
String — Default: basename(basename(tree,".nwk"),"_timetree")
???

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

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

4.6.2. Outputs

augur_export_only.auspice_json
File
???

augur_export_only.root_sequence_json
File
???

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