Mercurial > repos > peterjc > fastq_paired_unpaired
view tools/fastq_paired_unpaired/README.rst @ 6:f396701fbf32 draft
v0.1.3 Depends on Biopython 1.67 via Tool Shed package or bioconda.
author | peterjc |
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date | Wed, 10 May 2017 13:28:59 -0400 |
parents | b38bbcbd458d |
children | 2709a0f065c9 |
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Galaxy tool to divide FASTQ files into paired and unpaired reads ================================================================ This tool is copyright 2010-2017 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 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 Biopython, and allow you to 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). v0.1.2 - Belatedly declare Biopython dependency via Tool Shed. v0.1.3 - Minor internal changes to Python script for error reporting & style. - Updated to point at Biopython 1.67 (latest version in Tool Shed). - Explicit dependency on ``galaxy_sequence_utils``. ======= ====================================================================== 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 -t testtoolshed --check_diff tools/fastq_paired_unpaired/ ... or:: $ planemo shed_update -t toolshed --check_diff tools/fastq_paired_unpaired/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only 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.