Mercurial > repos > peterjc > seq_primer_clip
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 |
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date | Tue, 30 Apr 2013 11:04:43 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.txt.orig Tue Apr 30 11:04:43 2013 -0400 @@ -0,0 +1,103 @@ +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.