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  "Description": "Provides a set of utility function to prevent the spread\nof utility scripts in W4M (Workflow4Metabolomics) tools, and\ncentralize them in a single package. To note, some are meant to\nbe replaced by the use of dedicated packages in the future,\nlike the parse_args() function: it is here only to prepare the\nground for more global changes in W4M scripts and tools. This\npackage is used by part of the W4M Galaxy modules, some of them\nbeing available on the community-maintained GitHub repository\nfor Metabolomics' Galaxy tools\n<https://github.com/workflow4metabolomics/tools-metabolomics>.\nSee Delporte et al (2025) <doi:10.1002/cpz1.70095> for more\ndetails.",
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    "match2",
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    "optparse_character",
    "optparse_flag",
    "optparse_integer",
    "optparse_list",
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    "show_sys",
    "shy_lib",
    "source_local",
    "stock_id",
    "stopaste",
    "stopaste0",
    "stopf",
    "unmangle_galaxy_param",
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    "W4MLogger"
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      "title": "Check Errors",
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      "page": "check_one_character",
      "title": "check_one_character",
      "topics": [
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      "page": "check_one_complex",
      "title": "check_one_complex",
      "topics": [
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      ]
    },
    {
      "page": "check_one_integer",
      "title": "check_one_integer",
      "topics": [
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      ]
    },
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      "title": "check_one_logical",
      "topics": [
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      ]
    },
    {
      "page": "check_one_numeric",
      "title": "check_one_numeric",
      "topics": [
        "check_one_numeric"
      ]
    },
    {
      "page": "check_param_type_n_length",
      "title": "check_param_type_n_length - to check parameters",
      "topics": [
        "check_param_type_n_length"
      ]
    },
    {
      "page": "check_parameter_length",
      "title": "check_parameter_length - validate parameter's length",
      "topics": [
        "check_parameter_length"
      ]
    },
    {
      "page": "check_parameter_type",
      "title": "check_parameter_type - validate parameter's type",
      "topics": [
        "check_parameter_type"
      ]
    },
    {
      "page": "collapse",
      "title": "collapse - to paste strings with collapse = \"\"",
      "topics": [
        "collapse"
      ]
    },
    {
      "page": "collapse_lines",
      "title": "collapse_lines - to paste strings with collapse = \"\\n\"",
      "topics": [
        "collapse_lines"
      ]
    },
    {
      "page": "convert_parameters",
      "title": "Convert Parameters",
      "topics": [
        "convert_parameters"
      ]
    },
    {
      "page": "df_force_numeric",
      "title": "Convert data frame to numeric.",
      "topics": [
        "df_force_numeric"
      ]
    },
    {
      "page": "df_is",
      "title": "Test type of a data frame.",
      "topics": [
        "df_is"
      ]
    },
    {
      "page": "df_read_table",
      "title": "Data frame loading from a file.",
      "topics": [
        "df_read_table"
      ]
    },
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      "title": "Filtering tools for Galaxy scripting",
      "topics": [
        "Filtering_datasets"
      ]
    },
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      "page": "generic_filter",
      "title": "Filtering a data set following the 3-tables format",
      "topics": [
        "generic_filter"
      ]
    },
    {
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      "title": "get_base_dir - to get... the base directory",
      "topics": [
        "get_base_dir"
      ]
    },
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      "page": "get_logger",
      "title": "Instantiate a Logger",
      "topics": [
        "get_logger"
      ]
    },
    {
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      "title": "get_r_env - provides env vars begining with R_*",
      "topics": [
        "get_r_env"
      ]
    },
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      "title": "Import two W4M tables",
      "topics": [
        "import2"
      ]
    },
    {
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      "title": "Import the three W4M tables",
      "topics": [
        "import3"
      ]
    },
    {
      "page": "in_galaxy_env",
      "title": "in_galaxy_env - check if the script has been run by galaxy",
      "topics": [
        "in_galaxy_env"
      ]
    },
    {
      "page": "intens_check",
      "title": "Checking intensities of a data set following the W4M 3-tables format",
      "topics": [
        "intens_check"
      ]
    },
    {
      "page": "intensity_checks",
      "title": "Intensity checking tools for Galaxy scripting",
      "topics": [
        "intensity_checks"
      ]
    },
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      "title": "Table match check functions",
      "topics": [
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      ]
    },
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      "title": "match3",
      "topics": [
        "match3"
      ]
    },
    {
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      "title": "Merging a dataMatrix with a metadata file",
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    },
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      ]
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      "title": "optparse_integer - define a command parameter as an integer",
      "topics": [
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    },
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      "title": "optparse_list - define a command parameter as a list of objects",
      "topics": [
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      ]
    },
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      "page": "optparse_numeric",
      "title": "optparse_numeric - define a command parameter as an numeric",
      "topics": [
        "optparse_numeric"
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    },
    {
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      "title": "optparse_parameters - parse easily the command line parameters",
      "topics": [
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    },
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      "title": "Parse Command arguments",
      "topics": [
        "parse_args"
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    },
    {
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      "topics": [
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    },
    {
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      "title": "printfp - to paste, format and print a string",
      "topics": [
        "printfp"
      ]
    },
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      "title": "printp - to format a string and print it",
      "topics": [
        "printp"
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    },
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      "title": "Reproduce ID",
      "topics": [
        "reproduce_id"
      ]
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      "title": "run_galaxy_function - automate running functions in galaxy",
      "topics": [
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    },
    {
      "page": "run_galaxy_processing",
      "title": "run_galaxy_processing - automate running code in galaxy",
      "topics": [
        "run_galaxy_processing"
      ]
    },
    {
      "page": "show_galaxy_footer",
      "title": "show_galaxy_footer - shows the footer for glaxy tools",
      "topics": [
        "show_galaxy_footer"
      ]
    },
    {
      "page": "show_galaxy_header",
      "title": "show_galaxy_header - shows the header for glaxy tools",
      "topics": [
        "show_galaxy_header"
      ]
    },
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      "page": "show_sys",
      "title": "show_sys - prints env variables related to R",
      "topics": [
        "show_sys"
      ]
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      "title": "Shy Lib",
      "topics": [
        "shy_lib"
      ]
    },
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      "page": "source_local",
      "title": "source_local - source file, from absolute or relative path",
      "topics": [
        "source_local"
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      "page": "stock_id",
      "title": "Stock ID",
      "topics": [
        "stock_id"
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      "title": "stopaste - to paste string to a message and stop",
      "topics": [
        "stopaste"
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      "page": "stopaste0",
      "title": "stopaste0 - to paste string to a message and stop",
      "topics": [
        "stopaste0"
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      "page": "stopf",
      "title": "stopf - to stop and format message",
      "topics": [
        "stopf"
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      "title": "unmangle_galaxy_param - revert effects of galaxy manglings.",
      "topics": [
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      "page": "unmangle_galaxy_string",
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      "page": "W4MLogger",
      "title": "The W4MLogger Class",
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      "title": "W4MLogger_.message__",
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      "title": "Log info/warning/error/debug/verbose messages",
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        "W4MLogger$error",
        "W4MLogger$info",
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        "W4MLogger_[info,warning,error,debug,verbose]"
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      "page": "W4MLogger_set_verbose",
      "title": "W4MLogger$set_verbose",
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