Repository revision
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository 'fastq_paired_unpaired'
http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/7ed81e36fc1c
unrestricted
Divide FASTQ file into paired and unpaired reads
Using the common read name suffix conventions, it divides a FASTQ file into paired reads, and orphan or single reads.

The input file should be a valid FASTQ file which has been sorted so that any partner forward+reverse reads are consecutive. The output files all preserve this sort order. Pairings are recognised based on standard name suffices.

Any reads where the forward/reverse naming suffix used is not recognised are treated as orphan reads. The tool supports the old /1 and /2 convention used by Illumina, the new Illumina convention, the .f and .r convention, and the Sanger convention (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details).
1:7ed81e36fc1c
peterjc
True
314

Repository README files - may contain important installation or license information

Galaxy tool to divide FASTQ files into paired and unpaired reads ================================================================ 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 Biopython library functions) 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). 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. Simply add the line: That's it. History ======= 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 Developers ========== This script and other tools for filtering FASTA, FASTQ and SFF files are currently being developed on the following 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_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* Check this worked: $ tar -tzf fastq_paired_unpaired.tar.gz fastq/fastq_paired_unpaired.py fastq/fastq_paired_unpaired.txt fastq/fastq_paired_unpaired.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.

Contents of this repository

Name Description Version
Divide FASTQ file into paired and unpaired reads using the read name suffices 0.0.5

Automated tool test results

Time tested: 2014-02-13 13:01:21
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12484:b463c73f3348
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_paired_unpaired
Tool version: 0.0.5
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.5
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for fastq_paired_unpaired.

Categories
Text Manipulation
Sequence Analysis