.. _`bio/muscle`:

MUSCLE
======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/muscle?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/muscle

build multiple sequence alignments using MUSCLE.

**URL**: https://drive5.com/muscle5/manual/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule muscle_fasta:
        input:
            fasta="{sample}.fa",  # Input fasta file
        output:
            alignment="{sample}.fas",  # Output alignment file
        log:
            "logs/muscle/{sample}.log",
        params:
            extra="-refineiters 50",  # Additional arguments
        threads: 2
        wrapper:
            "v3.0.1/bio/muscle"


    rule muscle_super5:
        input:
            fasta="{sample}.fa",
        output:
            alignment="{sample}.super5.fas",
        log:
            "logs/muscle/{sample}.super5.log",
        params:
            super5 = True,
            extra="-refineiters 50",
        threads: 2
        wrapper:
            "v3.0.1/bio/muscle"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``muscle=5.1``

Input/Output
------------
**Input:**

* FASTA file

**Output:**

* Alignment file, with FASTA as default file format



Params
------

* ``super5``: specifies whether to use the Super5 algorithm to align sequences




Authors
-------

* Nikos Tsardakas Renhuldt


Code
----

.. code-block:: python

    __author__ = "Nikos Tsardakas Renhuldt"
    __copyright__ = "Copyright 2021, Nikos Tsardakas Renhuldt"
    __email__ = "nikos.tsardakas_renhuldt@tbiokem.lth.se"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")

    mode = "-align"
    if snakemake.params.get("super5"):
        mode = "-super5"

    shell(
        "muscle"
        " -threads {snakemake.threads}"
        " {mode} {snakemake.input.fasta}"
        " {extra}"
        " -output {snakemake.output.alignment}"
        " {log}"
    )


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