apply_config
Applies a FigTree JSON config and ordered clade operations to a phylogenetic tree, exporting Nexus. Validates parameters and runs operations in CLI order for agent-driven tweaks.
Instructions
Apply a FigTree JSON config (figtree-block keys) plus an ordered operations list and export Nexus. Leaner than style_tree for agent-driven advanced tweaks.
All accepted parameters are validated before execution (collapse_style,
multi_tree, auto_color_rank/collapse_rank and every operation
field); the execution order is annotations → auto-color/collapse-rank →
collapse operations, matching the CLI.
Args:
config: Any figtree-block key → value mapping (dot-separated keys).
operations: Ordered clade operations (same schema as style_tree).
taxonomy_levels: Custom rank prefixes (prefix:rank,...); active
during both loading and taxonomy analysis.
seed: Reproducible tree selection for multi_tree="random".
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | No | ||
| config | No | ||
| run_name | No | ||
| tree_file | No | ||
| multi_tree | No | ||
| operations | No | ||
| tree_index | No | ||
| tree_content | No | ||
| collapse_rank | No | ||
| collapse_style | No | collapse | |
| auto_color_rank | No | ||
| taxonomy_levels | No | ||
| taxonomy_mapping_file | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |