comparison tools/samtools_depad/README.rst @ 2:02572789ef6c draft

v0.0.4 Internal changes to command line handling

1:01f8967ce1e0

Galaxy wrapper for samtools depad
=================================

This wrapper 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.

This is a wrapper for part of the command line samtools suite, v0.1.19

This wrapper is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats


Automated Installation
======================

v0.0.1  - Initial public release.
v0.0.2  - Embed samtools citation in the tool XML.
        - Removed unused imports from Python wrapper script.
v0.0.3  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, 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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depad/
    ...

or::

    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depad/
    ...

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/samtools_depad/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/sam_spec_padded.bam
    test-data/sam_spec_padded.depad.bam
    test-data/sam_spec_padded.fasta

2:02572789ef6c

Galaxy wrapper for samtools depad
=================================

This wrapper 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.

This is a wrapper for part of the command line samtools suite, v0.1.19

This wrapper is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad


Automated Installation
======================

v0.0.1  - Initial public release.
v0.0.2  - Embed samtools citation in the tool XML.
        - Removed unused imports from Python wrapper script.
v0.0.3  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.0.4  - Use ``<command detect_errors="aggressive">`` (internal change only).
        - Single quote command line arguments (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/samtools_depad/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/samtools_depad/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/sam_spec_padded.bam
    test-data/sam_spec_padded.depad.bam
    test-data/sam_spec_padded.fasta