.. _`bio/fasttree`:

FASTTREE
========


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   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/fasttree

build phylogenetic trees using fasttree. Documentation found at http://www.microbesonline.org/fasttree/


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule fasttree:
        input:
            alignment="{sample}.fa",  # Input alignment file
        output:
            tree="{sample}.nwk",  # Output tree file
        log:
            "logs/muscle/{sample}.log",
        params:
            extra="",  # Additional arguments
        wrapper:
            "v3.0.1/bio/fasttree"

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.


Notes
-----

- fasttree can only be run with a single thread.


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

* ``fasttree=2.1.11``

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

* Alignment FASTA or interleaved phylip file

**Output:**

* Newick formatted tree file




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
    import os

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

    shell(
        "fasttree "
        "{extra} "
        "{snakemake.input.alignment} "
        "> {snakemake.output.tree} "
        "{log}"
    )


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