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W4MRUtils

• VERSION: 1.2.1

W4MRUtils is a R packages provided by W4M to ease galaxy toolswriting. It contains some utility functions that will help you in commontasks.

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 withunmangle_galaxy_param

Logfiles

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

TODO

Do the documentation and the referencing of the documentationfor:

• 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:

then

or

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

or

Uninstallation

You can uninstall the version of W4MRUtils you installed with:

or

>remove.packages("W4MRUtils")

XML Wrapper

Please followtheguidelines during the redaction of the xml wrapper.

Readthedoc in case of problems.