view tools/primers/seq_primer_clip.txt.orig @ 1:06e6112091aa draft

Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.

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

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

This tool is a short Python script (using the Galaxy library functions and
Biopython). 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/primers folder. You will also need to
modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
this to tools_conf.xml.sample in order to run the tests:

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

There are optionally some example files required to run the functional tests,
put these in the test-data/primers folder.

test-data/primers/dop_primers.fasta
test-data/primers/MID4_GLZRM4E04_rnd30.fasta
test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
test-data/primers/MID4_GLZRM4E04_rnd30.sff
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff

You should then be able to run the tests with:

sh run_functional_tests.sh -id seq_primer_clip

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


History
=======

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.


Developers
==========

This script and related tools are being developed on the following hg branch:
http://bitbucket.org/peterjc/galaxy-central/src/tools

This incorporates the previously used hg branch:
http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder:

$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/*

Check this worked:

$ tar -tzf seq_primer_clip.tar.gz
tools/primers/seq_primer_clip.py
tools/primers/seq_primer_clip.txt
tools/primers/seq_primer_clip.xml
test-data/primers/dop_primers.fasta
test-data/primers/MID4_GLZRM4E04_rnd30.fasta
test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta
test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff
test-data/primers/MID4_GLZRM4E04_rnd30.sff


Licence (MIT/BSD style)
=======================

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.