Mercurial > repos > peterjc > fastq_paired_unpaired
diff tools/fastq_paired_unpaired/README.rst @ 4:09f9f0e29e47 draft
v0.0.6 use format_source; v0.0.5 error handling & citation
author | peterjc |
---|---|
date | Wed, 05 Aug 2015 11:06:38 -0400 |
parents | |
children | b38bbcbd458d |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq_paired_unpaired/README.rst Wed Aug 05 11:06:38 2015 -0400 @@ -0,0 +1,131 @@ +Galaxy tool to divide FASTQ files into paired and unpaired reads +================================================================ + +This tool is copyright 2010-2015 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 which divides a FASTQ file into paired +reads, and single or orphan reads. You can have separate files for the +forward/reverse reads, or have them interleaved in a single file. + +Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even +Color Space should all work equally well). + +This tool is available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired + + +Automated Installation +====================== + +This should be straightforward, Galaxy should automatically download and install +the tool from the Galaxy Tool Shed, and run the unit tests + + +Manual Installation +=================== + +There are just two files to install: + +* ``fastq_paired_unpaired.py`` (the Python script) +* ``fastq_paired_unpaired.xml`` (the Galaxy tool definition) + +The suggested location is in the Galaxy folder tools/fastq next to other FASTQ +tools provided with Galaxy. + +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer +the tool. One suggested location is next to the ``fastq_filter.xml`` entry, or use +a dedicated folder like ``tools/fastq_paired_unpaired``. Then simply add the line:: + + <tool file="fastq_paired_unpaired/fastq_paired_unpaired.xml" /> + +That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version, using Biopython +v0.0.2 - Help text; cope with multiple pairs per template +v0.0.3 - Galaxy XML wrappers added +v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency) +v0.0.5 - Handle Illumina 1.8 style pair names +v0.0.6 - Record script version when run from Galaxy + - Added unit test (FASTQ file using Sanger naming) +v0.0.7 - Link to Tool Shed added to help text and this documentation. +v0.0.8 - Use reStructuredText for this README file. + - Adopt standard MIT License. + - Updated citation information (Cock et al. 2013). + - Development moved to GitHub. +v0.0.9 - Renamed folder and adopted README.rst naming. + - Removed some unused code in the Python script. +v0.1.0 - Switch to using Biopython (easier to use script outside of Galaxy). + - Leaves FASTQ plus lines blank (smaller output files). + - Tool definition now embeds citation information. +v0.1.1 - Reorder XML elements (internal change only). + - Use ``format_source=...`` tag. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +======= ====================================================================== + + +Developers +========== + +This script and other tools for filtering FASTA, FASTQ and SFF files were +initially developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter + +Development has now moved to a dedicated GitHub repository: +https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired + +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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ + ... + +or:: + + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/sanger-pairs-forward.fastq + test-data/sanger-pairs-interleaved.fastq + test-data/sanger-pairs-mixed.fastq + test-data/sanger-pairs-reverse.fastq + test-data/sanger-pairs-singles.fastq + tools/fastq_paired_unpaired/README.rst + tools/fastq_paired_unpaired/fastq_paired_unpaired.py + tools/fastq_paired_unpaired/fastq_paired_unpaired.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.