1"""Snakemake wrapper for clustal omega."""
2# Snakemake wrappers are provided by Truwl to teach the internal mechanics of Snakemake recipes. View https://github.com/snakemake/snakemake-wrappers to learn how to use wrappers.
3
4__author__ = "Michael Hall"
5__copyright__ = "Copyright 2019, Michael Hall"
6__email__ = "mbhall88@gmail.com"
7__license__ = "MIT"
8
9
10from snakemake.shell import shell
11
12# Placeholder for optional parameters
13extra = snakemake.params.get("extra", "")
14# Formats the log redrection string
15log = snakemake.log_fmt_shell(stdout=True, stderr=True)
16
17# Executed shell command
18shell(
19    "clustalo {extra}"
20    " --threads={snakemake.threads}"
21    " --in {snakemake.input[0]}"
22    " --out {snakemake.output[0]} "
23    " {log}"
24)
25