fast_nnt/
cli.rs

1use clap::{Args, Parser, Subcommand};
2
3use crate::{ordering::OrderingMethod, weights::active_set_weights::NNLSParams};
4
5#[derive(Parser, Debug)]
6#[command(version, about, long_about = None)]
7pub struct ProgramArgs {
8    #[command(subcommand)]
9    pub subcommand: ProgramSubcommand,
10    #[arg(
11        short,
12        long,
13        default_value = "1",
14        global = true,
15        help = "Number of threads to use."
16    )]
17    pub threads: usize,
18    #[arg(
19        short,
20        long,
21        default_value = "false",
22        conflicts_with = "quiet",
23        global = true
24    )]
25    pub verbose: bool,
26    #[arg(
27        short,
28        long,
29        default_value = "false",
30        conflicts_with = "verbose",
31        global = true
32    )]
33    pub quiet: bool,
34    #[arg(
35        short = 'd',
36        long,
37        default_value = "output",
38        global = true,
39        help = "Output directory"
40    )]
41    pub output_directory: String,
42}
43
44#[derive(Subcommand, Debug)]
45pub enum ProgramSubcommand {
46    #[clap(
47        name = "neighbour_net",
48        about = "Run the SplitsTree NeighborNet algorithm"
49    )]
50    NeighborNet(NeighbourNetArgs),
51}
52
53#[derive(Args, Debug)]
54pub struct NeighbourNetArgs {
55    /// Input distance matrix file path
56    #[arg(short, long, help = "Input distance matrix file path", required = true)]
57    pub input: String,
58    #[arg(
59        short,
60        long,
61        help = "Output prefix for result files",
62        default_value = "output"
63    )]
64    pub output_prefix: String,
65    #[arg(
66        short = 'O',
67        long,
68        help = "The ordering algorithm to use to get splits cycle",
69        default_value = "splits-tree4"
70    )]
71    pub ordering: OrderingMethod,
72    #[clap(flatten)]
73    pub nnls_params: NNLSParams,
74}
75
76impl NeighbourNetArgs {
77    pub fn default() -> Self {
78        Self {
79            input: String::new(),
80            output_prefix: String::from("output"),
81            ordering: OrderingMethod::SplitsTree4,
82            nnls_params: NNLSParams::default(),
83        }
84    }
85}
fast_nnt/cli.rs

fast_nnt/
cli.rs
