- VERSION: 1.0.0
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.
- Parsing parameters with parse_args (easier)
- Parsing parameters with optparse_parameters (better)
- Enforce checking on parameters with check_param_type_n_length
- Silently load a package with shy_lib
- Sourcing relative file with source_local
- 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
- 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)
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
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');"
You can uninstall the version of W4MRUtils you installed with:
$ make remove_package
or
> remove.packages("W4MRUtils")
Please follow the guidelines during the redaction of the xml wrapper.
Read the doc in case of problems.