generate.full.commands: Generate full commands

In kstagaman/sharpton-lab-metaGTx.processing: Sharpton Lab Metagenomic & Metatranscriptomic Processing

Generate full commands

Description

This function generates a single-line tool command with the supplied parameters for each file in the supplied directory as well as appending other commands, such as gzipping and moving results files.

Usage

generate.full.commands(
  input.dir = NULL,
  paired = TRUE,
  tmp.dir = NULL,
  output.dir = ".",
  prepend = NULL,
  src.tool.path = NULL,
  zip.output = TRUE,
  write.to = NULL,
  ...
)

Arguments

input.dir	character; path to directory containing input files. Default is NULL.
paired	logical; are their paired R1 and R2 files that should be analyzed concurrently? Default is TRUE.
tmp.dir	character; path to temporary directory for direct output. After files are written here, they will be moved to output.dir. Default is NULL.
output.dir	character; path to storage directory for output. If no tmp.dir output will be written here, otherwise it will be written to tmp.dir first and then moved here. Default is '.'.
prepend	character; any command you want run before the rest of the full command. Default is NULL.
src.tool.path	character; path to script for sourcing tool, if required by system, this will also append the command source <PATH> ; to the full commands. NULL means this is not prepended. Default is NULL.
zip.output	logical; whether to gzip final output (occurs before moving files if tmp.dir is set). Default is TRUE.
write.to	character; file name to write commands to, if NULL, only returns commands as character vector. Default is NULL
...	other commands to pass to appropriate tool. Names must match short or long version found in that tool's help page.

See Also

system, list2, generate.tool.command

kstagaman/sharpton-lab-metaGTx.processing documentation built on Oct. 2, 2022, 4:39 p.m.