Mercurial > repos > peterjc > seq_select_by_id
diff tools/filters/seq_select_by_id.txt @ 0:838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:38 -0400 |
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children | 50a8a6917a9c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/seq_select_by_id.txt Tue Jun 07 17:43:38 2011 -0400 @@ -0,0 +1,78 @@ +Galaxy tool to select FASTA, FASTQ or SFF sequences by ID +========================================================= + +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 Biopython library functions) to extract +sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given +by a column of a tabular file. The output order follows that of the tabular file, +and if there are duplicates in the tabular file, there will be duplicates in the +output sequence file. + +See also the sister tool to filter sequence files according to IDs from column(s) +of a tabular file, where the output order follows the sequence file, and any +duplicate IDs are ignored. + +There are just two files to install: + +* seq_select_by_id.py (the Python script) +* seq_select_by_id.xml (the Galaxy tool definition) + +The suggested location is in the Galaxy folder tools/filters next to the tool +for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. One suggested location is in the filters section. Simply add the line: + +<tool file="filters/sff_select_by_id.xml" /> + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +v0.0.1 - Initial version. + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* + +Check this worked: + +$ tar -tzf seq_select_by_id.tar.gz +filter/seq_select_by_id.py +filter/seq_select_by_id.txt +filter/seq_select_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.