check_err |
Check Errors |
check_one_character |
check_one_character |
check_one_complex |
check_one_complex |
check_one_integer |
check_one_integer |
check_one_logical |
check_one_logical |
check_one_numeric |
check_one_numeric |
check_parameter_length |
check_parameter_length - validate parameter's length |
check_parameter_type |
check_parameter_type - validate parameter's type |
check_param_type_n_length |
check_param_type_n_length - to check parameters |
collapse |
collapse - to paste strings with collapse = "" |
collapse_lines |
collapse_lines - to paste strings with collapse = "\n" |
convert_parameters |
Convert Parameters |
df_force_numeric |
Convert data frame to numeric. |
df_is |
Test type of a data frame. |
df_read_table |
Data frame loading from a file. |
get_base_dir |
get_base_dir - to get... the base directory |
get_logger |
Instantiate a Logger |
get_r_env |
get_r_env - provides env vars begining with R_* |
import2 |
Import two W4M tables |
import3 |
Import the three W4M tables |
in_galaxy_env |
in_galaxy_env - check if the script has been run by galaxy |
match2 |
Table match check functions |
match3 |
match3 |
mini_tools |
Mini tools for Galaxy scripting |
optparse_character |
optparse_character - define a command parameter as string |
optparse_flag |
optparse_flag - define a command parameter as a trigger |
optparse_integer |
optparse_integer - define a command parameter as an integer |
optparse_list |
optparse_list - define a command parameter as a list of objects |
optparse_numeric |
optparse_numeric - define a command parameter as an numeric |
optparse_parameters |
optparse_parameters - parse easily the command line parameters |
parse_args |
Parse Command arguments |
printf |
printf - to format a string and print it |
printfp |
printfp - to paste, format and print a string |
printp |
printp - to format a string and print it |
reproduce_id |
Reproduce ID |
run_galaxy_function |
run_galaxy_function - automate running functions in galaxy |
run_galaxy_processing |
run_galaxy_processing - automate running code in galaxy |
show_galaxy_footer |
show_galaxy_footer - shows the footer for glaxy tools |
show_galaxy_header |
show_galaxy_header - shows the header for glaxy tools |
show_sys |
show_sys - prints env variables related to R |
shy_lib |
Shy Lib |
source_local |
source_local - source file, from absolute or relative path |
stock_id |
Stock ID |
stopaste |
stopaste - to paste string to a message and stop |
stopaste0 |
stopaste0 - to paste string to a message and stop |
stopf |
stopf - to stop and format message |
unmangle_galaxy_param |
unmangle_galaxy_param - revert effects of galaxy manglings. |
unmangle_galaxy_string |
unmangle_galaxy_string - revert effects of galaxy mangling |
W4MLogger |
The W4MLogger Class |
W4MLogger$debug |
Log info/warning/error/debug/verbose messages |
W4MLogger$error |
Log info/warning/error/debug/verbose messages |
W4MLogger$info |
Log info/warning/error/debug/verbose messages |
W4MLogger$verbose |
Log info/warning/error/debug/verbose messages |
W4MLogger$warning |
Log info/warning/error/debug/verbose messages |
W4MLogger_.message__ |
W4MLogger_.message__ |
W4MLogger_add_out_paths |
Adds a file where logs are duplicated |
W4MLogger_finalize |
W4MLogger_finalize |
W4MLogger_set_debug |
W4MLogger$set_debug |
W4MLogger_set_error |
W4MLogger$set_error |
W4MLogger_set_info |
W4MLogger$set_info |
W4MLogger_set_out_paths |
Defines in which file logs are duplicated |
W4MLogger_set_verbose |
W4MLogger$set_verbose |
W4MLogger_set_warning |
W4MLogger$set_warning |
W4MLogger_[info,warning,error,debug,verbose] |
Log info/warning/error/debug/verbose messages |