Mercurial > repos > peterjc > fastq_filter_by_id
comparison tools/fastq/fastq_filter_by_id.txt @ 0:10e963c79a45
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 17:23:26 -0400 |
| parents | |
| children | d570cc324779 |
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| -1:000000000000 | 0:10e963c79a45 |
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| 1 Galaxy tool to filter FASTQ sequences by ID | |
| 2 =========================================== | |
| 3 | |
| 4 This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. | |
| 5 See the licence text below. | |
| 6 | |
| 7 This tool is a short Python script (using the Galaxy library functions) which | |
| 8 divides a FASTQ file in two, those sequences with or without an ID present in | |
| 9 the specified column(s) of a tabular file. Example uses include filtering based | |
| 10 on search results from a tool like NCBI BLAST before assembly. | |
| 11 | |
| 12 There are just two files to install: | |
| 13 | |
| 14 * fastq_filter_by_id.py (the Python script) | |
| 15 * fastq_filter_by_id.xml (the Galaxy tool definition) | |
| 16 | |
| 17 The suggested location is next to the similarly named fastq_filter.py and | |
| 18 fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy | |
| 19 folder tools/fastq | |
| 20 | |
| 21 You will also need to modify the tools_conf.xml file to tell Galaxy to offer | |
| 22 the tool. The suggested location is next to the fastq_filter.xml entry. Simply | |
| 23 add the line: | |
| 24 | |
| 25 <tool file="fastq/fastq_filter_by_id.xml" /> | |
| 26 | |
| 27 That's it. | |
| 28 | |
| 29 | |
| 30 History | |
| 31 ======= | |
| 32 | |
| 33 v0.0.1 - Initial verion (not publicly released) | |
| 34 v0.0.2 - Allow both, just pos or just neg output files | |
| 35 - Preserve the FASTQ variant in the XML wrapper | |
| 36 | |
| 37 | |
| 38 Developers | |
| 39 ========== | |
| 40 | |
| 41 This script and similar versions for FASTA and SFF files are currently being | |
| 42 developed on the following hg branch: | |
| 43 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | |
| 44 | |
| 45 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
| 46 the following command from the Galaxy root folder: | |
| 47 | |
| 48 tar -czf fastq_filter_by_id.tar.gz tools/fastq/fastq_filter_by_id.* | |
| 49 | |
| 50 Check this worked: | |
| 51 | |
| 52 $ tar -tzf fastq_filter_by_id.tar.gz | |
| 53 fastq/fastq_filter_by_id.py | |
| 54 fastq/fastq_filter_by_id.txt | |
| 55 fastq/fastq_filter_by_id.xml | |
| 56 | |
| 57 | |
| 58 Licence (MIT/BSD style) | |
| 59 ======================= | |
| 60 | |
| 61 Permission to use, copy, modify, and distribute this software and its | |
| 62 documentation with or without modifications and for any purpose and | |
| 63 without fee is hereby granted, provided that any copyright notices | |
| 64 appear in all copies and that both those copyright notices and this | |
| 65 permission notice appear in supporting documentation, and that the | |
| 66 names of the contributors or copyright holders not be used in | |
| 67 advertising or publicity pertaining to distribution of the software | |
| 68 without specific prior permission. | |
| 69 | |
| 70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 77 OR PERFORMANCE OF THIS SOFTWARE. |