Mercurial > repos > peterjc > fastq_filter_by_id
view tools/fastq/fastq_filter_by_id.txt @ 2:d570cc324779
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:24:08 -0400 |
parents | 10e963c79a45 |
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Obsolete ======== This tool is now obsolete, having been replaced by a more general version covering the FASTA, FASTQ and SFF sequence formats in a single tool.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 FASTQ sequences by ID =========================================== This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. See the licence text below. This tool is a short Python script (using the Galaxy library functions) which divides a FASTQ 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 before assembly. There are just two files to install: * fastq_filter_by_id.py (the Python script) * fastq_filter_by_id.xml (the Galaxy tool definition) The suggested location is next to the similarly named fastq_filter.py and fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy folder tools/fastq 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 fastq_filter.xml entry. Simply add the line: <tool file="fastq/fastq_filter_by_id.xml" /> That's it. History ======= v0.0.1 - Initial verion (not publicly released) v0.0.2 - Allow both, just pos or just neg output files - Preserve the FASTQ variant in the XML wrapper v0.0.3 - Fixed bug when generating non-matching FASTQ file only v0.0.4 - Deprecated, marked as hidden in the XML 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://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: tar -czf fastq_filter_by_id.tar.gz tools/fastq/fastq_filter_by_id.* Check this worked: $ tar -tzf fastq_filter_by_id.tar.gz fastq/fastq_filter_by_id.py fastq/fastq_filter_by_id.txt fastq/fastq_filter_by_id.xml 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.