Workflow input using a grover API — tar_input

Targets for workflow inputs using a grover API

Usage

tar_input_grover(
  name,
  instrument,
  experiment,
  grover_client,
  conversion_args = grover::conversionArgsPeakPick(),
  data_dir = "data/mzML"
)

Arguments

name: Symbol. The name for the collection of targets. This serves as a prefix for target names.
instrument: The grover API repository instrument name.
experiment: The experiment name referring to a directory available on the grover API.
grover_client: S4 object of class GroverClient specifying the host details of the grover API.
conversion_args: The file conversion arguments to be passed to the args argument of grover::convertFile().
data_dir: The path to the directory in which to output converted mzML files.

Value

A list of target objects specifically for analysis pipeline input using the specified grover API.

Examples

## Grover API input
targets::tar_dir({
targets::tar_script({
    library(hrmtargets)
    list(
        tar_input_grover(example,
                         'an_instrument',
                         'an_experiment',
                         grover::grover('a_host',80,'1234'))
)
})
targets::tar_manifest()
})
#> # A tibble: 4 × 3
#>   name                           command                                 pattern
#>   <chr>                          <chr>                                   <chr>  
#> 1 example_raw_files              "grover::listRawFiles(new(\"GroverClie… NA     
#> 2 example_raw_sample_information "grover::sampleInfo(new(\"GroverClient… map(ex…
#> 3 example_mzML                   "grover::convertFile(new(\"GroverClien… map(ex…
#> 4 example_sample_information     "metaboMisc::convertSampleInfo(example… NA