.. _`bio/clustalo`:

CLUSTALO
========


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

Multiple alignment of nucleic acid and protein sequences.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule clustalo:
        input:
            "{sample}.fa"
        output:
            "{sample}.msa.fa"
        params:
            extra=""
        log:
            "logs/clustalo/test/{sample}.log"
        threads: 8
        wrapper:
            "v3.0.1/bio/clustalo"

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
---------------------

* ``clustalo=1.2.4``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    """Snakemake wrapper for clustal omega."""

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2019, Michael Hall"
    __email__ = "mbhall88@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    # Formats the log redrection string
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Executed shell command
    shell(
        "clustalo {extra}"
        " --threads={snakemake.threads}"
        " --in {snakemake.input[0]}"
        " --out {snakemake.output[0]} "
        " {log}"
    )


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