comparison tools/sample_seqs/README.rst @ 6:31f5701cd2e9 draft

v0.2.4 Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.

5:6b71ad5d43fb

Galaxy tool to sub-sample sequence files
========================================

This tool is copyright 2014-2015 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 (using Biopython library functions)
to sub-sample sequence files (in a range of formats including FASTA, FASTQ,

v0.2.2  - Reorder XML elements (internal change only).
        - Use ``format_source=...`` tag.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.2.3  - Do the Biopython imports at the script start (internal change only).
        - Clarify paired read example in help text.
======= ======================================================================


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 ~/repositories/pico_galaxy/tools/sample_seqs/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/
    ...

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/sample_seqs/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff

6:31f5701cd2e9

Galaxy tool to sub-sample sequence files
========================================

This tool is copyright 2014-2017 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 (using Biopython library functions)
to sub-sample sequence files (in a range of formats including FASTA, FASTQ,

v0.2.2  - Reorder XML elements (internal change only).
        - Use ``format_source=...`` tag.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.2.3  - Do the Biopython imports at the script start (internal change only).
        - Clarify paired read example in help text.
v0.2.4  - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
        - Style changes to Python code (internal change only).
======= ======================================================================


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/sample_seqs/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/sample_seqs/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff