RSEMflow command-line entry point — cli

Parses rsemflow <module> <action> [options] and calls the matching R function. Options use the prefixes --i- (inputs), --m- (metadata), --p- (parameters), and --o- (outputs). Add --help at any level for usage.

Usage

cli_main(args = commandArgs(trailingOnly = TRUE))

Arguments

args: Character vector of command-line arguments.

Value

Invisibly returns zero on success. Errors are raised as R errors.

Details

The installed launcher script (system.file("exec", "rsemflow", package = "rsemflow")) calls this function. Without the launcher, use Rscript -e "rsemflow::cli_main()" <module> <action> [options].

Examples

cli_main("--help")
#> RSEMflow - metadata-driven downstream analysis for RSEM gene-level results
#> 
#> Usage:
#>   rsemflow <module> <action> [options]
#> 
#> Modules and actions:
#>   data          import, summarize
#>   annotation    ensembl, gtf
#>   expression    normalize, pca, correlation
#>   differential  deseq2
#>   enrichment    gsea, gsva
#> 
#> Option grammar:
#>   --i-*   input data
#>   --m-*   metadata
#>   --p-*   analysis parameters
#>   --o-*   outputs
#> 
#> Examples:
#>   rsemflow data import --help
#>   rsemflow differential deseq2 --help
#>   rsemflow enrichment gsea --help
#> 
#> Version:
#>   0.1.1
cli_main(c("differential", "deseq2", "--help"))
#> Run metadata-driven DESeq2 differential expression.
#> 
#> Usage:
#>   rsemflow differential deseq2 [options]
#> 
#> Inputs:
#>   --i-study                Input study directory or study.rds. [required]
#> 
#> Metadata:
#>   --m-metadata             Optional replacement TSV/CSV metadata.
#> 
#> Parameters:
#>   --p-formula              Design formula, e.g. '~ batch + condition'. [required]
#>   --p-term                 Metadata term to report/test. [required]
#>   --p-reference            Reference as COLUMN::LEVEL; repeatable. [repeatable]
#>   --p-contrast             Explicit comparison COLUMN::NUMERATOR::DENOMINATOR; repeatable. [repeatable]
#>   --p-at                   Condition a simple effect as COLUMN::LEVEL; currently one value. [repeatable]
#>   --p-categorical          Metadata column to force categorical; repeatable. [repeatable]
#>   --p-numeric              Metadata column to force numeric; repeatable. [repeatable]
#>   --p-test                 wald or lrt. [default: wald]
#>   --p-reduced              Reduced formula required for lrt.
#>   --p-alpha                DESeq2 alpha threshold. [default: 0.05]
#> 
#> Outputs:
#>   --o-differential         Output directory. [required]
#>