gtars/gtars-cli/src/genomicdist/cli.rs at 78bd3e42dc5598857793730e28d2bdb757c36278 · databio/gtars · GitHub

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use clap::{Arg, Command, arg};

pub const GENOMICDIST_CMD: &str = "genomicdist";

pub fn create_genomicdist_cli() -> Command {
    Command::new(GENOMICDIST_CMD)
        .about("Compute genomic distribution statistics for a BED file.")
        .arg(
            arg!(--bed <BED>)
                .required(true)
                .help("Path to input BED file"),
        )
        .arg(
            arg!(--gtf <GTF>)
                .required(false)
                .help("Path to GTF/GTF.gz gene model (enables partitions; also TSS distances if no --tss)"),
        )
        .arg(
            arg!(--tss <TSS>)
                .required(false)
                .help("Path to TSS BED file (overrides GTF-derived TSS for distance calculation)"),
        )
        .arg(
            Arg::new("chrom-sizes")
                .long("chrom-sizes")
                .required(false)
                .help("Path to chrom.sizes file (enables expected partitions and promoter trimming)"),
        )
        .arg(
            arg!(--output <OUTPUT>)
                .required(false)
                .help("Output JSON path (default: stdout)"),
        )
        .arg(
            arg!(--bins <BINS>)
                .required(false)
                .default_value("250")
                .help("Number of bins for region distribution"),
        )
        .arg(
            Arg::new("signal-matrix")
                .long("signal-matrix")
                .required(false)
                .help("Path to open signal matrix TSV (enables cell-type open chromatin enrichment)"),
        )
        .arg(
            Arg::new("promoter-upstream")
                .long("promoter-upstream")
                .required(false)
                .default_value("200")
                .help("Upstream distance (bp) from TSS to define promoter regions"),
        )
        .arg(
            Arg::new("promoter-downstream")
                .long("promoter-downstream")
                .required(false)
                .default_value("2000")
                .help("Downstream distance (bp) from TSS to define promoter regions"),
        )
        .arg(
            Arg::new("compact")
                .long("compact")
                .action(clap::ArgAction::SetTrue)
                .help("Compact JSON output (default: pretty-printed)"),
        )
}