generate.tool.command: Generate tool command

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

Generate tool command

Description

This function generates a character string of a command given a tool and its arguments.

Usage

generate.tool.command(tool, tool.path = NULL, ...)

Arguments

tool	character; name of the appropriate tool, e.g. "kneaddata" or "humann".
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.
...	other commands to pass to appropriate tool. Names must match short or long version found in that tool's help page. If the flag takes no argument in the tool, pass "flag" to the argument. E.g. for bash command ls -l you could run generate.tool.command(tool = "ls", l = "flag")

See Also

system, list2

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