setFastSeqDump: Create a fastSeqDump object Users have the option of...

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

Create a fastSeqDump object Users have the option of downloading SRA data using fastq-dump or FTP.

Usage

setFastSeqDump(
  sampleURLs,
  outDir,
  validate = FALSE,
  sampleList,
  useFastqDump = FALSE,
  fastqDumpPath = NA_character_,
  install_dump = FALSE
)

Arguments

sampleURLs	OPTIONAL input. Path to text file containing FTP URLs generated from SRA Explorer. If this parameter is provided, then fastqDumpPath is ignored.
outDir	Required input. Path to write output files.
validate	Default is FALSE. When TRUE, all validation methods are executed
sampleList	Required input if fastqDumpPath is specified. New-line delimited text file containin SRA accession IDs.
useFastqDump	If TRUE, Fastq-dump will be used in place of wget. Requires fastqDumpPath to be supplied. If not present, fastq-dump present in system.files will be used.
fastqDumpPath	Set path to fastq-dump script. If provided, fastq-dump is used in place of wget/curl. TODO: Add Example

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.