external_tools_add_tool_to_dataframe: external_tools_add_tool_to_dataframe

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

external_tools_add_tool_to_dataframe

Description

Appends tool metadata on the end of a dataframe

Usage

external_tools_add_tool_to_dataframe(
  external_tools_df = dplyr::tibble(),
  tool_name,
  tool_id,
  tool_group,
  tool_class,
  tool_description,
  instructions = "No instructions available yet. You're on your own buddy",
  platform = "Web App",
  website,
  doi,
  requires_maf_export = TRUE,
  requires_gene_selection = FALSE,
  maf_conversion_function = NA,
  extension = "tsv"
)

Arguments

external_tools_df	the dataframe to add tool metadata to. By default, will create and return a new dataframe
tool_name	name of tool (string)
tool_id	id of tool (string)
tool_group	research group that built/maintains the tool (string)
tool_class	class of tool. Usually 'Positive Selection', 'Variant Interpretation' (string)
tool_description	brief description of tool (string)
instructions	brief description of how to use the tool. Any HTML tags in the string will be correctly resolved. (string)
platform	what platform do we access the tool from. Examples include web, desktop app, cli (string)
website	url of tool (string)
doi	publicatoin doi (string)
requires_maf_export	does the tool require a maf to be exported in some other form (flag)
requires_gene_selection	does user need to select a specific gene for export to work? (bool)
maf_conversion_function	only relevent if requires_maf_export == true. A function that takes a maf_dataset_wrapper object (first argument), a filepath (second argument) and, if requires_gene_selection == TRUE, a gene name (third argument) writes a file to that filepath. The idea is that said file can then be used as input to the specified tool.
extension	what type of file is written by maf_conversion_function. default is 'tsv'. Used to appropriately name exported file (string)

Value

dataframe containing external_tool_metadata

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.