comparison tools/fastq_paired_unpaired/README.rst @ 6:f396701fbf32 draft

v0.1.3 Depends on Biopython 1.67 via Tool Shed package or bioconda.

5:b38bbcbd458d

Galaxy tool to divide FASTQ files into paired and unpaired reads
================================================================

This tool is copyright 2010-2015 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below (MIT licence).

This tool is a short Python script which divides a FASTQ file into paired
reads, and single or orphan reads. You can have separate files for the

        - Tool definition now embeds citation information.
v0.1.1  - Reorder XML elements (internal change only).
        - Use ``format_source=...`` tag.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.1.2  - Belatedly declare Biopython dependency via Tool Shed.
======= ======================================================================


Developers
==========

For pushing a release to the test or main "Galaxy Tool Shed", use the following
Planemo commands (which requires you have set your Tool Shed access details in
``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
    ...

or::

    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/sanger-pairs-forward.fastq
    test-data/sanger-pairs-interleaved.fastq
    test-data/sanger-pairs-mixed.fastq

6:f396701fbf32

Galaxy tool to divide FASTQ files into paired and unpaired reads
================================================================

This tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below (MIT licence).

This tool is a short Python script which divides a FASTQ file into paired
reads, and single or orphan reads. You can have separate files for the

        - Tool definition now embeds citation information.
v0.1.1  - Reorder XML elements (internal change only).
        - Use ``format_source=...`` tag.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.1.2  - Belatedly declare Biopython dependency via Tool Shed.
v0.1.3  - Minor internal changes to Python script for error reporting & style.
        - Updated to point at Biopython 1.67 (latest version in Tool Shed).
        - Explicit dependency on ``galaxy_sequence_utils``.
======= ======================================================================


Developers
==========

For pushing a release to the test or main "Galaxy Tool Shed", use the following
Planemo commands (which requires you have set your Tool Shed access details in
``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

    $ planemo shed_update -t testtoolshed --check_diff tools/fastq_paired_unpaired/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff tools/fastq_paired_unpaired/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only tools/fastq_paired_unpaired/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/sanger-pairs-forward.fastq
    test-data/sanger-pairs-interleaved.fastq
    test-data/sanger-pairs-mixed.fastq