comparison tools/get_orfs_or_cdss/README.rst @ 9:a06ad07431ba draft

v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.

8:09a8be9247ca

Galaxy tool to find ORFs or simple CDSs
=======================================

This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
Additions copyright 2015-2016 by Eric Rasche.
See the licence text below (MIT licence).

This tool is a short Python script (using Biopython library functions)

v0.1.0  - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
        - Using ``optparse`` for the Python command line API (Eric Rasche).
        - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
v0.1.1  - Reorder XML elements (internal change only).
v0.2.0  - Tool now also outputs GFF3 formatted calls (Eric Rasche).
======= ======================================================================


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/get_orfs_or_cdss/
    ...

or::

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

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/Ssuis.fasta
    test-data/get_orf_input.Suis_ORF.bed
    test-data/get_orf_input.Suis_ORF.nuc.fasta

9:a06ad07431ba

Galaxy tool to find ORFs or simple CDSs
=======================================

This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
Additions copyright 2015-2016 by Eric Rasche.
See the licence text below (MIT licence).

This tool is a short Python script (using Biopython library functions)

v0.1.0  - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
        - Using ``optparse`` for the Python command line API (Eric Rasche).
        - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
v0.1.1  - Reorder XML elements (internal change only).
v0.2.0  - Tool now also outputs GFF3 formatted calls (Eric Rasche).
v0.2.1  - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
        - Added NCBI genetic code table 24, Candidate Division SR1 and
	  Gracilibacteria.
======= ======================================================================


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/get_orfs_or_cdss/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/get_orfs_or_cdss/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/Ssuis.fasta
    test-data/get_orf_input.Suis_ORF.bed
    test-data/get_orf_input.Suis_ORF.nuc.fasta