Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
===========================================================

This tool is copyright 2011-2017 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 the Galaxy library functions and
Biopython). It is available from the Galaxy Tool Shed here:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip


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

This should be straightforward using the Galaxy Tool Shed, which should be
able to automatically install the dependency on Biopython, and then install
this tool and run its unit tests.


Manual Installation
===================

There are just two files to install:

* ``seq_primer_clip.py`` (the Python script)
* ``seq_primer_clip.xml`` (the Galaxy tool definition)

The suggested location is a new ``tools/seq_primer_clip/`` folder. You will
also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
tool::

  <tool file="seq_primer_clip/seq_primer_clip.xml" />

If you wish to run the unit tests, also move/copy the ``test-data/`` files
under Galaxy's ``test-data/`` folder. Then::

    $ ./run_tests.sh -id seq_primer_clip

You will also need to install Biopython 1.54 or later. That's it.


History
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.1  - Initial version (not publicly released)
v0.0.2  - Sort primers by length (longest and therefore most specific first)
v0.0.3  - Consider missing bases at start/end of read as mismatches
v0.0.4  - Apply minimum length to sequences with no match too
v0.0.5  - Count clipped & non-matched short reads separately, length bug fixes
v0.0.6  - Added some functional tests
v0.0.7  - Added error check for bad filename arguments
v0.0.8  - Record version of Python script when run from Galaxy.
        - Check for errors using Python script's return code.
v0.0.9  - Moved test data to workaround Galaxy Tool Shed limititation.
v0.0.10 - Include links to Tool Shed in help text and this README file.
        - Use reStructuredText for this README file.
        - Adopted standard MIT licence.
        - Automated installation of Biopython dependency.
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
        - Renamed folder and adopted README.rst naming.
v0.0.11 - Correct automated dependency definition.
v0.0.12 - Simplified XML to apply input format to output data.
        - Tool definition now embeds citation information.
v0.0.13 - Use ``format_source=...`` tag.
        - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Fixed input file help text.
v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
        - Explicit dependency on ``galaxy_sequence_utils``.
v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only).
        - Single quote command line arguments (internal change only)
v0.0.16 - Python 3 compatible print function.
======= ======================================================================


Developers
==========

This script and related tools were initially developed on the following hg branches:
http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy


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/seq_primer_clip/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/seq_primer_clip/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/MID4_GLZRM4E04_rnd30.fasta
    test-data/MID4_GLZRM4E04_rnd30.fastqsanger
    test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
    test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
    test-data/MID4_GLZRM4E04_rnd30_fclip.sff
    test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
    test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
    test-data/MID4_GLZRM4E04_rnd30.sff
    test-data/dop_primers.fasta
    tools/seq_primer_clip/README.rst
    tools/seq_primer_clip/seq_primer_clip.py
    tools/seq_primer_clip/seq_primer_clip.xml
    tools/seq_primer_clip/tool_dependencies.xml


Licence (MIT)
=============

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.