diff tools/primers/seq_primer_clip.txt.orig @ 1:8c02a91a8680 draft

Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
author peterjc
date Tue, 30 Apr 2013 11:04:43 -0400
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+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.