feat: Add markdown help option and documentation for deepbiop-cli

crates/deepbiop-cli/Cargo.toml

@@ -30,6 +30,7 @@ clap-verbosity-flag = "3.0"
 ctrlc = "3.4"
 human-panic = "2.0"
 env_logger = "0.11.6"
+clap-markdown = "0.1.4"
 
 [[bin]]
 path = "src/main.rs"

crates/deepbiop-cli/src/main.rs

@@ -24,6 +24,9 @@ struct Cli {
 
     #[command(flatten)]
     verbose: clap_verbosity_flag::Verbosity,
+
+    #[arg(long, hide = true)]
+    markdown_help: bool,
 }
 
 #[derive(Subcommand, Debug)]
@@ -107,6 +110,11 @@ fn main() -> Result<()> {
         return Ok(());
     }
 
+    if cli.markdown_help {
+        clap_markdown::print_help_markdown::<Cli>();
+        return Ok(());
+    }
+
     match &cli.command {
         Some(Commands::CountChimeric(count_chimeric)) => {
             count_chimeric.run().unwrap();

docs/cli/index.md

@@ -0,0 +1,256 @@
+# Command-Line Help for `deepbiop-cli`
+
+This document contains the help content for the `deepbiop-cli` command-line program.
+
+**Command Overview:**
+
+* [`deepbiop-cli`↴](#deepbiop-cli)
+* [`deepbiop-cli count-chimeric`↴](#deepbiop-cli-count-chimeric)
+* [`deepbiop-cli bam-to-fq`↴](#deepbiop-cli-bam-to-fq)
+* [`deepbiop-cli fq-to-fa`↴](#deepbiop-cli-fq-to-fa)
+* [`deepbiop-cli fa-to-fq`↴](#deepbiop-cli-fa-to-fq)
+* [`deepbiop-cli fa-to-parquet`↴](#deepbiop-cli-fa-to-parquet)
+* [`deepbiop-cli fq-to-parquet`↴](#deepbiop-cli-fq-to-parquet)
+* [`deepbiop-cli extract-fq`↴](#deepbiop-cli-extract-fq)
+* [`deepbiop-cli extract-fa`↴](#deepbiop-cli-extract-fa)
+* [`deepbiop-cli fqs-to-one`↴](#deepbiop-cli-fqs-to-one)
+* [`deepbiop-cli fas-to-one`↴](#deepbiop-cli-fas-to-one)
+
+## `deepbiop-cli`
+
+CLI tool for Processing Biological Data.
+
+**Usage:** `deepbiop-cli [OPTIONS] [COMMAND]`
+
+###### **Subcommands:**
+
+* `count-chimeric` — Count chimeric reads in a BAM file
+* `bam-to-fq` — BAM to fastq conversion
+* `fq-to-fa` — Fastq to fasta conversion
+* `fa-to-fq` — Fasta to fastq conversion
+* `fa-to-parquet` — Fasta to parquet conversion
+* `fq-to-parquet` — Fastq to parquet conversion
+* `extract-fq` — Extract fastq reads from a fastq file
+* `extract-fa` — Extract fasta reads from a fasta file
+* `fqs-to-one` — Multiple Fastqs to one Fastq conversion
+* `fas-to-one` — Multiple Fastas to one Fasta conversion
+
+###### **Options:**
+
+* `--generate <GENERATOR>`
+
+  Possible values: `bash`, `elvish`, `fish`, `powershell`, `zsh`
+
+* `-v`, `--verbose` — Increase logging verbosity
+* `-q`, `--quiet` — Decrease logging verbosity
+
+
+
+## `deepbiop-cli count-chimeric`
+
+Count chimeric reads in a BAM file
+
+**Usage:** `deepbiop-cli count-chimeric [OPTIONS] [bam]...`
+
+###### **Arguments:**
+
+* `<bam>` — path to the bam file
+
+###### **Options:**
+
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli bam-to-fq`
+
+BAM to fastq conversion
+
+**Usage:** `deepbiop-cli bam-to-fq [OPTIONS] [bam]...`
+
+###### **Arguments:**
+
+* `<bam>` — path to the bam file
+
+###### **Options:**
+
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+* `-c`, `--compressed` — output bgzip compressed fastq file
+
+
+
+## `deepbiop-cli fq-to-fa`
+
+Fastq to fasta conversion
+
+**Usage:** `deepbiop-cli fq-to-fa [OPTIONS] [fq]...`
+
+###### **Arguments:**
+
+* `<fq>` — path to the fq file
+
+###### **Options:**
+
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli fa-to-fq`
+
+Fasta to fastq conversion
+
+**Usage:** `deepbiop-cli fa-to-fq [OPTIONS] [fa]...`
+
+###### **Arguments:**
+
+* `<fa>` — path to the fa file
+
+###### **Options:**
+
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli fa-to-parquet`
+
+Fasta to parquet conversion
+
+**Usage:** `deepbiop-cli fa-to-parquet [OPTIONS] <fa>`
+
+###### **Arguments:**
+
+* `<fa>` — path to the fa file
+
+###### **Options:**
+
+* `--chunk` — if convert the fa file to parquet by chunk or not
+* `--chunk-size <CHUNK_SIZE>` — chunk size
+
+  Default value: `1000000`
+* `--output <result>` — result path
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli fq-to-parquet`
+
+Fastq to parquet conversion
+
+**Usage:** `deepbiop-cli fq-to-parquet [OPTIONS] <fq>`
+
+###### **Arguments:**
+
+* `<fq>` — path to the fq file
+
+###### **Options:**
+
+* `--chunk` — if convert the fq file to parquet by chunk or not
+* `--chunk-size <CHUNK_SIZE>` — chunk size
+
+  Default value: `1000000`
+* `--output <output>` — result path
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli extract-fq`
+
+Extract fastq reads from a fastq file
+
+**Usage:** `deepbiop-cli extract-fq [OPTIONS] <fq>`
+
+###### **Arguments:**
+
+* `<fq>` — path to the fq file
+
+###### **Options:**
+
+* `--reads <reads>` — Path to the selected reads
+* `--number <number>` — The number of selected reads by random
+* `--output <output>` — output bgzip compressed file
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+* `-c`, `--compressed` — output bgzip compressed fastq file
+
+
+
+## `deepbiop-cli extract-fa`
+
+Extract fasta reads from a fasta file
+
+**Usage:** `deepbiop-cli extract-fa [OPTIONS] <fa>`
+
+###### **Arguments:**
+
+* `<fa>` — path to the bam file
+
+###### **Options:**
+
+* `--reads <reads>` — Path to the selected reads
+* `--number <number>` — The number of selected reads by random
+* `--output <output>` — output bgzip compressed file
+* `-t`, `--threads <THREADS>` — threads number
+
+  Default value: `2`
+* `-c`, `--compressed` — output bgzip compressed fasta file
+
+
+
+## `deepbiop-cli fqs-to-one`
+
+Multiple Fastqs to one Fastq conversion
+
+**Usage:** `deepbiop-cli fqs-to-one [OPTIONS] --output <output> [fqs]...`
+
+###### **Arguments:**
+
+* `<fqs>` — path to the fq file
+
+###### **Options:**
+
+* `--output <output>` — output bgzip compressed file
+* `-t`, `--threads <THREADS>`
+
+  Default value: `2`
+
+
+
+## `deepbiop-cli fas-to-one`
+
+Multiple Fastas to one Fasta conversion
+
+**Usage:** `deepbiop-cli fas-to-one [OPTIONS] --output <output> [fas]...`
+
+###### **Arguments:**
+
+* `<fas>` — path to the fa file
+
+###### **Options:**
+
+* `--output <output>` — output bgzip compressed file
+* `-t`, `--threads <THREADS>`
+
+  Default value: `2`
+
+
+
+<hr/>
+
+<small><i>
+    This document was generated automatically by
+    <a href="https://crates.io/crates/clap-markdown"><code>clap-markdown</code></a>.
+</i></small>
+

mkdocs.yml

@@ -18,6 +18,8 @@ nav:
           - development/versioning.md
   - API reference:
       - api/index.md
+  - CLI:
+      - cli/index.md
   - About:
       - License: license.md