.. _`bio/bustools/text`:

BUSTOOLS TEXT
=============


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

convert bus to tsv files

**URL**: https://github.com/BUStools/bustools#text

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_bustools_text:
        input:
            "file.bus",
        output:
            "file.tsv",
        threads: 1
        params:
            extra="",
        log:
            "logs/bustools.log",
        wrapper:
            "v3.0.1/bio/bustools/text"


    rule test_bustools_text_list:
        input:
            ["file.bus", "file2.bus"],
        output:
            "file2.tsv",
        threads: 1
        params:
            extra="--flags --pad",
        log:
            "logs/bustools.log",
        wrapper:
            "v3.0.1/bio/bustools/text"

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
-----

When multiple bus files are provided, only one TSV file is produced.

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

* ``bustools=0.43.1``

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

* list of bus files

**Output:**

* Path to TSV output



Params
------

* ``extra``: Optional parameters, besides `--o/-output`




Authors
-------



Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # conding: utf-8

    """snakemake wrapper for bustool text"""


    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    bus_files = snakemake.input[0]
    if isinstance(bus_files, list):
        bus_files = " ".join(bus_files)

    shell("bustools text --output {snakemake.output[0]} {extra} {bus_files} {log}")


.. |nl| raw:: html

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