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adjust clap help message
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@endixk
endixk committed Feb 10, 2025
1 parent 1fb1593 commit 50b0e25
Showing 1 changed file with 136 additions and 134 deletions.
270 changes: 136 additions & 134 deletions src/util/arg_parser.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ use crate::util::arg_parser::Commands::*;

#[derive(Parser)]
#[clap(disable_version_flag = true, arg_required_else_help = true)]
#[command(subcommand_value_name = "MODULE")]
pub struct ClapArgs {
#[command(subcommand)]
pub command: Option<Commands>,
Expand Down Expand Up @@ -43,7 +44,142 @@ const GENETREE_HELP: &str = cstr!(r#"<bold><underline>Example:</underline></bold
<bold>unicore gene-tree --realign --threshold 30 --name /path/to/hashed/gene/names example/tree</bold>
"#);
#[derive(Subcommand)]
#[command(subcommand_help_heading = "Modules")]
pub enum Commands {
/// Easy core gene phylogeny workflow, from fasta files to phylogenetic tree
#[clap(arg_required_else_help = true, allow_hyphen_values = true)]
EasyCore {
/// Input directory with fasta files or a single fasta file
input: PathBuf,
/// Output directory where all results will be saved
output: PathBuf,
/// ProstT5 model
model: PathBuf,
/// tmp directory
tmp: PathBuf,
/// Keep intermediate files
#[arg(short, long, default_value="false")]
keep: bool,
/// Force overwrite output database
#[arg(short='w', long, default_value="false")]
overwrite: bool,
/// Set maximum sequence length threshold
#[arg(long)]
max_len: Option<usize>,
/// Use GPU for foldseek createdb
#[arg(short, long, default_value="false")]
gpu: bool,
/// Use python script instead. hidden option
#[arg(long, default_value="true", hide = true)]
use_python: bool,
/// Use foldseek for createdb. hidden option
#[arg(long, default_value="false", hide = true)]
use_foldseek: bool,
/// Use AFDB lookup for foldseek createdb. Useful for large databases
#[arg(long, default_value="false")]
afdb_lookup: bool,
/// Local path to the directory with AFDB lookup tables. hidden option
#[arg(long, hide = false)]
afdb_local: Option<PathBuf>,
/// Arguments for foldseek options in string e.g. -c "-c 0.8"
#[arg(short, long, default_value="-c 0.8")]
cluster_options: String,
/// Coverage threshold for core structures. [0 - 100]
#[arg(short='C', long, default_value="80", value_parser = threshold_in_range)]
core_threshold: usize,
/// Generate tsv with copy number statistics
#[arg(short, long, default_value="true")]
print_copiness: bool,
/// Multiple sequence aligner [foldmason, mafft-linsi, mafft]
#[arg(short='A', long, default_value="foldmason")]
aligner: String,
/// Phylogenetic tree builder [iqtree, fasttree (under development), raxml (under development)]
#[arg(short='T', long, default_value="iqtree")]
tree_builder: String,
/// Options for sequence aligner
#[arg(short, long)]
aligner_options: Option<String>,
/// Options for tree builder; please adjust if using different tree method
#[arg(short, long, default_value="-m JTT+F+I+G -B 1000")]
tree_options: String,
/// Gap threshold for multiple sequence alignment [0 - 100]
#[arg(short='G', long, default_value="50", value_parser = threshold_in_range)]
gap_threshold: usize,
/// Number of threads to use; 0 to use all
#[arg(long, default_value="0")]
threads: usize,
/// Verbosity (0: quiet, 1: +errors, 2: +warnings, 3: +info, 4: +debug)
#[arg(short='v', long, default_value="3")]
verbosity: u8,
},
/// Easy search workflow, from fasta files to phylogenetic tree
#[clap(arg_required_else_help = true, allow_hyphen_values = true, hide = true)]
EasySearch {
/// Input directory with fasta files or a single fasta file
input: PathBuf,
/// Target database to search against
target: PathBuf,
/// Output directory where all results will be saved
output: PathBuf,
/// ProstT5 model
model: PathBuf,
/// tmp directory
tmp: PathBuf,
/// Keep intermediate files
#[arg(short, long, default_value="false")]
keep: bool,
/// Force overwrite output database
#[arg(short='w', long, default_value="false")]
overwrite: bool,
/// Set maximum sequence length threshold
#[arg(long)]
max_len: Option<usize>,
/// Use GPU for foldseek createdb
#[arg(short, long, default_value="false")]
gpu: bool,
/// Use python script instead. hidden option
#[arg(long, default_value="true", hide = true)]
use_python: bool,
/// Use foldseek for createdb. hidden option
#[arg(long, default_value="false", hide = true)]
use_foldseek: bool,
/// Use AFDB lookup for foldseek createdb. Useful for large databases
#[arg(long, default_value="false")]
afdb_lookup: bool,
/// Local path to the directory with AFDB lookup tables. hidden option
#[arg(long, hide = true)]
afdb_local: Option<PathBuf>,
/// Arguments for foldseek options in string e.g. -s "-c 0.8"
#[arg(short, long, default_value="-c 0.8")]
search_options: String,
/// Coverage threshold for core structures. [0 - 100]
#[arg(short='C', long, default_value="80", value_parser = threshold_in_range)]
core_threshold: usize,
/// Generate tsv with copy number statistics
#[arg(short, long, default_value="true")]
print_copiness: bool,
/// Multiple sequence aligner [foldmason, mafft-linsi, mafft]
#[arg(short='A', long, default_value="foldmason")]
aligner: String,
/// Phylogenetic tree builder [iqtree, fasttree (under development), raxml (under development)]
#[arg(short='T', long, default_value="iqtree")]
tree_builder: String,
/// Options for sequence aligner
#[arg(short, long)]
aligner_options: Option<String>,
/// Options for tree builder; please adjust if using different tree method
#[arg(short, long, default_value="-m JTT+F+I+G -B 1000")]
tree_options: String,
/// Gap threshold for multiple sequence alignment [0 - 100]
#[arg(short='G', long, default_value="50", value_parser = threshold_in_range)]
gap_threshold: usize,
/// Number of threads to use; 0 to use all
#[arg(long, default_value="0")]
threads: usize,
/// Verbosity (0: quiet, 1: +errors, 2: +warnings, 3: +info, 4: +debug)
#[arg(short='v', long, default_value="3")]
verbosity: u8,
},
/// Create Foldseek database from amino acid sequences
#[clap(arg_required_else_help = true, allow_hyphen_values = true, verbatim_doc_comment)]
Createdb {
Expand Down Expand Up @@ -226,140 +362,6 @@ pub enum Commands {
#[arg(short='v', long, default_value="3")]
verbosity: u8,
},
/// Easy core gene phylogeny workflow, from fasta files to phylogenetic tree
#[clap(arg_required_else_help = true, allow_hyphen_values = true)]
EasyCore {
/// Input directory with fasta files or a single fasta file
input: PathBuf,
/// Output directory where all results will be saved
output: PathBuf,
/// ProstT5 model
model: PathBuf,
/// tmp directory
tmp: PathBuf,
/// Keep intermediate files
#[arg(short, long, default_value="false")]
keep: bool,
/// Force overwrite output database
#[arg(short='w', long, default_value="false")]
overwrite: bool,
/// Set maximum sequence length threshold
#[arg(long)]
max_len: Option<usize>,
/// Use GPU for foldseek createdb
#[arg(short, long, default_value="false")]
gpu: bool,
/// Use python script instead. hidden option
#[arg(long, default_value="true", hide = true)]
use_python: bool,
/// Use foldseek for createdb. hidden option
#[arg(long, default_value="false", hide = true)]
use_foldseek: bool,
/// Use AFDB lookup for foldseek createdb. Useful for large databases
#[arg(long, default_value="false")]
afdb_lookup: bool,
/// Local path to the directory with AFDB lookup tables. hidden option
#[arg(long, hide = false)]
afdb_local: Option<PathBuf>,
/// Arguments for foldseek options in string e.g. -c "-c 0.8"
#[arg(short, long, default_value="-c 0.8")]
cluster_options: String,
/// Coverage threshold for core structures. [0 - 100]
#[arg(short='C', long, default_value="80", value_parser = threshold_in_range)]
core_threshold: usize,
/// Generate tsv with copy number statistics
#[arg(short, long, default_value="true")]
print_copiness: bool,
/// Multiple sequence aligner [foldmason, mafft-linsi, mafft]
#[arg(short='A', long, default_value="foldmason")]
aligner: String,
/// Phylogenetic tree builder [iqtree, fasttree (under development), raxml (under development)]
#[arg(short='T', long, default_value="iqtree")]
tree_builder: String,
/// Options for sequence aligner
#[arg(short, long)]
aligner_options: Option<String>,
/// Options for tree builder; please adjust if using different tree method
#[arg(short, long, default_value="-m JTT+F+I+G -B 1000")]
tree_options: String,
/// Gap threshold for multiple sequence alignment [0 - 100]
#[arg(short='G', long, default_value="50", value_parser = threshold_in_range)]
gap_threshold: usize,
/// Number of threads to use; 0 to use all
#[arg(long, default_value="0")]
threads: usize,
/// Verbosity (0: quiet, 1: +errors, 2: +warnings, 3: +info, 4: +debug)
#[arg(short='v', long, default_value="3")]
verbosity: u8,
},
/// Easy search workflow, from fasta files to phylogenetic tree
#[clap(arg_required_else_help = true, allow_hyphen_values = true, hide = true)]
EasySearch {
/// Input directory with fasta files or a single fasta file
input: PathBuf,
/// Target database to search against
target: PathBuf,
/// Output directory where all results will be saved
output: PathBuf,
/// ProstT5 model
model: PathBuf,
/// tmp directory
tmp: PathBuf,
/// Keep intermediate files
#[arg(short, long, default_value="false")]
keep: bool,
/// Force overwrite output database
#[arg(short='w', long, default_value="false")]
overwrite: bool,
/// Set maximum sequence length threshold
#[arg(long)]
max_len: Option<usize>,
/// Use GPU for foldseek createdb
#[arg(short, long, default_value="false")]
gpu: bool,
/// Use python script instead. hidden option
#[arg(long, default_value="true", hide = true)]
use_python: bool,
/// Use foldseek for createdb. hidden option
#[arg(long, default_value="false", hide = true)]
use_foldseek: bool,
/// Use AFDB lookup for foldseek createdb. Useful for large databases
#[arg(long, default_value="false")]
afdb_lookup: bool,
/// Local path to the directory with AFDB lookup tables. hidden option
#[arg(long, hide = true)]
afdb_local: Option<PathBuf>,
/// Arguments for foldseek options in string e.g. -s "-c 0.8"
#[arg(short, long, default_value="-c 0.8")]
search_options: String,
/// Coverage threshold for core structures. [0 - 100]
#[arg(short='C', long, default_value="80", value_parser = threshold_in_range)]
core_threshold: usize,
/// Generate tsv with copy number statistics
#[arg(short, long, default_value="true")]
print_copiness: bool,
/// Multiple sequence aligner [foldmason, mafft-linsi, mafft]
#[arg(short='A', long, default_value="foldmason")]
aligner: String,
/// Phylogenetic tree builder [iqtree, fasttree (under development), raxml (under development)]
#[arg(short='T', long, default_value="iqtree")]
tree_builder: String,
/// Options for sequence aligner
#[arg(short, long)]
aligner_options: Option<String>,
/// Options for tree builder; please adjust if using different tree method
#[arg(short, long, default_value="-m JTT+F+I+G -B 1000")]
tree_options: String,
/// Gap threshold for multiple sequence alignment [0 - 100]
#[arg(short='G', long, default_value="50", value_parser = threshold_in_range)]
gap_threshold: usize,
/// Number of threads to use; 0 to use all
#[arg(long, default_value="0")]
threads: usize,
/// Verbosity (0: quiet, 1: +errors, 2: +warnings, 3: +info, 4: +debug)
#[arg(short='v', long, default_value="3")]
verbosity: u8,
},
}

#[derive(Default)]
Expand Down

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