Utils List for W4M - Workflow for Metabolomics.

W4MRUtils

• 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.

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.