Useful Functions for Harmonized W4M Tool Development

Provides a set of utility function to prevent the spread of utility scripts in W4M (Workflow4Metabolomics) tools, and centralize them in a single package. To note, some are meant to be replaced by the use of dedicated packages in the future, like the parse_args() function: it is here only to prepare the ground for more global changes in W4M scripts and tools. This package is used by part of the W4M Galaxy modules, some of them being available on the community-maintained GitHub repository for Metabolomics' Galaxy tools < https://github.com/workflow4metabolomics/tools-metabolomics>. See Delporte et al (2025) for more details.

W4MRUtils

• VERSION: 1.2.2

W4MRUtils is a R packages provided by W4M to ease galaxy tools writing. It contains some utility functions that will help you in common tasks.

Parameters

• Parsing parameters with parse_args (easier)
• Parsing parameters with optparse_parameters (better)
• Enforce checking on parameters with check_param_type_n_length

R script chores

• Silently load a package with shy_lib
• Sourcing relative file with source_local

Galaxy

• Am I in a galaxy env? see in_galaxy_env
• Show log headers with show_galaxy_header
• Show log footer with show_galaxy_footer
• Execute a function with run_galaxy_processing
• Restore parameters names, modified by galaxy with unmangle_galaxy_param

Logfiles

• What is a logger? - See logging section what-is-a-logger)
• How to create a logger? - See logging section how-to-create-a-logger)
• How to create a log file? - See logging section how-to-create-a-log-file)

TODO

Do the documentation and the referencing of the documentation for:

• stock_id
• reproduce_id
• check_err
• match2
• match3
• import2
• import3
• df_is
• df_force_numeric
• df_read_table

Installation

You can install the development version of W4MRUtils like so:

$ git clone https://github.com/workflow4metabolomics/W4MRUtils
$ cd W4MRUtils

then

$ make install

or

> rmarkdown::render("README.Rmd")
> devtools::document(".")
> roxygen2::roxygenize(".")
> devtools::test(".")
> devtools::install(".", dependencies = FALSE, repos = NULL, type = "source")

or

$ R -q -e "install.packages('W4MRUtils', repos='https://cran.irsn.fr');"

Uninstallation

You can uninstall the version of W4MRUtils you installed with:

$ make remove_package

or

> remove.packages("W4MRUtils")

XML Wrapper

Please follow the guidelines during the redaction of the xml wrapper.

Read the doc in case of problems.