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Sync CLI to Cargo.toml #39

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160 changes: 77 additions & 83 deletions src/cli.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,3 @@
name: Rust-Bio-Tools
author: Johannes Köster <[email protected]>
about: A set of ultra-fast command line utilities for bioinformatics tasks based on Rust-Bio.

settings:
- SubcommandRequired

Expand Down Expand Up @@ -41,7 +37,6 @@ subcommands:
required: true
help: File with list of record IDs to remove, one per line.


- bam-depth:
about: |
Print depth of BAM or CRAM file at given positions from STDIN (tab separated: chrom, pos).
Expand Down Expand Up @@ -77,7 +72,7 @@ subcommands:
long: incl-flags
short: i
value_name: INT
help: "Skip reads with mask bits unset []."
help: "Skip reads with mask bits unset []."
- exclude-flags:
long: excl-flags
short: e
Expand Down Expand Up @@ -168,32 +163,33 @@ subcommands:
author: Johannes Köster <[email protected]>, Jan Forster <[email protected]>

- vcf-annotate-dgidb:
about: |
Looks for interacting drugs in DGIdb and annotates them for every gene in every record.
about: |
Looks for interacting drugs in DGIdb and annotates them for every gene in every record.

Example:
rbt vcf-annotate-dgidb input.vcf > output.vcf
args:
- vcf:
required: true
help: VCF/BCF file to be extended by dgidb drug entries
- api-path:
long: api-path
short: p
default_value: http://dgidb.org/api/v2/interactions.json?genes=
help: url prefix for requesting interaction drugs by gene names.
- field:
long: field
short: f
default_value: dgiDB_drugs
help: Info field name to be used for annotation.
- genes-per-request:
long: genes-per-request
short: g
default_value: "1000"
help: Number of genes to submit per api request. A lower value increases the number of api requests in return.
Too many requests could be rejected by the DGIdb server.
author: Felix Mölder <[email protected]>
Example:
rbt vcf-annotate-dgidb input.vcf > output.vcf
args:
- vcf:
required: true
help: VCF/BCF file to be extended by dgidb drug entries
- api-path:
long: api-path
short: p
default_value: http://dgidb.org/api/v2/interactions.json?genes=
help: url prefix for requesting interaction drugs by gene names.
- field:
long: field
short: f
default_value: dgiDB_drugs
help: Info field name to be used for annotation.
- genes-per-request:
long: genes-per-request
short: g
default_value: "1000"
help:
Number of genes to submit per api request. A lower value increases the number of api requests in return.
Too many requests could be rejected by the DGIdb server.
author: Felix Mölder <[email protected]>

- call-consensus-reads:
about: |
Expand Down Expand Up @@ -226,56 +222,56 @@ subcommands:
{n}
author: Johannes Köster <[email protected]>, Henning Timm <[email protected]>, Felix Mölder <[email protected]>
args:
- fq1:
required: true
help: Input FASTQ file with forward reads.
- fq2:
required: true
help: Input FASTQ file with reverse reads.
- consensus-fq1:
required: true
help: Output FASTQ file with forward reads.
- consensus-fq2:
required: true
help: Output FASTQ file with reverse reads.
- consensus-fq3:
requires: [insert-size, std-dev]
help: Output FASTQ file for overlapping consensus reads (Required for calculating overlapping consensus only)
- max-umi-dist:
long: max-umi-dist
short: d
default_value: "1"
help: Maximum hamming distance between the UMIs of any pair of reads in the same cluster.
- umi-len:
long: umi-len
short: l
default_value: "8"
help: Length of UMI in read.
- max-seq-dist:
long: max-seq-dist
short: D
possible_values: ["1", "2", "3", "4", "5", "6", "7", "8"]
default_value: "2"
help: Maximum hamming distance between the sequences of any pair of reads in the same cluster.
- umi-on-reverse:
long: umi-on-reverse
short: u
help: Set if UMI is on reverse read
- verbose-read-names:
long: verbose-read-names
help: Add list of reads that were merged for each consensus read. Note that this can yield very long FASTQ name lines which cannot be handled by some tools.
- insert-size:
long: insert-size
short: i
takes_value: true
requires: [consensus-fq3, std-dev]
help: Expected insert size of sequenced fragment (Required for calculating overlapping consensus only)
- std-dev:
long: std-dev
short: s
takes_value: true
requires: [consensus-fq3, insert-size]
help: Standard deviation of expected insert size. Defines search space of the most likely overlap. (Required for calculating overlapping consensus only)
- fq1:
required: true
help: Input FASTQ file with forward reads.
- fq2:
required: true
help: Input FASTQ file with reverse reads.
- consensus-fq1:
required: true
help: Output FASTQ file with forward reads.
- consensus-fq2:
required: true
help: Output FASTQ file with reverse reads.
- consensus-fq3:
requires: [insert-size, std-dev]
help: Output FASTQ file for overlapping consensus reads (Required for calculating overlapping consensus only)
- max-umi-dist:
long: max-umi-dist
short: d
default_value: "1"
help: Maximum hamming distance between the UMIs of any pair of reads in the same cluster.
- umi-len:
long: umi-len
short: l
default_value: "8"
help: Length of UMI in read.
- max-seq-dist:
long: max-seq-dist
short: D
possible_values: ["1", "2", "3", "4", "5", "6", "7", "8"]
default_value: "2"
help: Maximum hamming distance between the sequences of any pair of reads in the same cluster.
- umi-on-reverse:
long: umi-on-reverse
short: u
help: Set if UMI is on reverse read
- verbose-read-names:
long: verbose-read-names
help: Add list of reads that were merged for each consensus read. Note that this can yield very long FASTQ name lines which cannot be handled by some tools.
- insert-size:
long: insert-size
short: i
takes_value: true
requires: [consensus-fq3, std-dev]
help: Expected insert size of sequenced fragment (Required for calculating overlapping consensus only)
- std-dev:
long: std-dev
short: s
takes_value: true
requires: [consensus-fq3, insert-size]
help: Standard deviation of expected insert size. Defines search space of the most likely overlap. (Required for calculating overlapping consensus only)
- bam:
about: |
Tool to remove PCR duplicates from BAM file.
Expand Down Expand Up @@ -304,5 +300,3 @@ subcommands:
- verbose-read-names:
long: verbose-read-names
help: Add list of reads that were merged for each consensus read. Note that this can yield very long FASTQ name lines which cannot be handled by some tools.


7 changes: 6 additions & 1 deletion src/main.rs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
//! Documentation for Rust Bio Tools
#[macro_use]
extern crate clap;
use clap::{load_yaml, value_t};
use log::LevelFilter;

Expand All @@ -15,7 +17,10 @@ pub mod fastq;
fn main() -> Result<(), Box<dyn Error>> {
let yaml = load_yaml!("cli.yaml");
let matches = App::from_yaml(yaml)
.version(env!("CARGO_PKG_VERSION"))
.name(crate_name!())
.author(crate_authors!())
.version(crate_version!())
.about(crate_description!())
.get_matches();

fern::Dispatch::new()
Expand Down