bowtie2: BLASTM Client

In gotoolchest/toolchest-client-r: R Client for Toolchest

BLASTM Client

Description

Runs BLASTN via Toolchest.

Starts a query for Bowtie 2 (for alignment) using Toolchest.

Usage

bowtie2(
  tool_args = "",
  inputs,
  output_path = NULL,
  database_name = "GRCh38_noalt_as",
  database_version = "1",
  ...
)

bowtie2(
  tool_args = "",
  inputs,
  output_path = NULL,
  database_name = "GRCh38_noalt_as",
  database_version = "1",
  ...
)

Arguments

tool_args	(optional) Additional arguments to be passed to Bowtie 2.
inputs	Path or list of paths to be passed in as input.
output_path	(optional) Path to a directory where the output file(s) will be downloaded.
database_name	(optional) Name of database to use for Bowtie 2 alignment. Uses the GRCh38 no-alt analysis set ("GRCh38_noalt_as") by default. Index files generated by the Langmead lab.
database_version	(optional) Version of database to use for Bowtie 2 alignment. Defaults to "1".
output_primary_name	(optional) Base name of output file. Defaults to blastn_results_out.
is_async	(optional) Whether to run a job asynchronously. Defaults to false.

Details

If output_path is left unspecified, downloading will be skipped.

If output_path is left unspecified, downloading will be skipped.

Value

Reference to an object with output location data.

Reference to an object with output location data.

gotoolchest/toolchest-client-r documentation built on July 14, 2022, 7 a.m.