Mercurial > repos > peterjc > fasta_filter_by_id
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v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author | peterjc |
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date | Fri, 03 Feb 2017 05:32:34 -0500 |
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Obsolete ======== This tool is now obsolete, having been replaced by a more general version covering the FASTA, FASTQ and SFF sequence formats in a single tool. You should only install this tool if you need to support existing workflows which used it. Galaxy tool to filter FASTA sequences by ID =========================================== 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 (using the Galaxy library functions) which divides a FASTA file in two, those sequences with or without an ID present in the specified column(s) of a tabular file. Example uses include filtering based on search results from a tool like NCBI BLAST, TMHMM or SignalP. There are just two files to install: * fasta_filter_by_id.py (the Python script) * fasta_filter_by_id.xml (the Galaxy tool definition) The suggested location is next to the similarly named fasta_filter_by_length.py and fasta_filter_by_length.xml files which are included with Galaxy, i.e. in the Galaxy folder tools/fasta_tools You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. The suggested location is next to the fasta_filter_by_length.xml entry. Simply add the line: <tool file="fasta_tools/fasta_filter_by_id.xml" /> That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial version (not publicly released) v0.0.2 - Allow both, just pos or just neg output files v0.0.3 - Include FASTA in tool name v0.0.4 - Deprecated, marked as hidden in the XML v0.0.5 - Explicit dependency on ``galaxy_sequence_utils``. - Citation information (Cock et al. 2013). - Explicitly record version via ``<version_command>``. - Use standard MIT license (was previously using the MIT/BSD style Biopython Licence Agreement). ======= ====================================================================== Developers ========== This script and other tools for filtering FASTA, FASTQ and SFF files were initially developed on the following hg branches: http://bitbucket.org/peterjc/galaxy-central/src/tools http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter It is now under GitHub https://github.com/peterjc/pico_galaxy/ 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/fasta_filter_by_id/ ... or:: $ planemo shed_update -t toolshed --check_diff tools/fasta_filter_by_id/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only tools/fasta_filter_by_id/ ... $ tar -tzf shed_upload.tar.gz tools/fasta_filter_by_id/README.rst tools/fasta_filter_by_id/fasta_filter_by_id.py tools/fasta_filter_by_id/fasta_filter_by_id.xml tools/fasta_filter_by_id/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/blastp_four_human_vs_rhodopsin.tabular test-data/four_human_proteins_filter_a.fasta test-data/four_human_proteins_filter_b.fasta 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.