view tools/fastq/fastq_paired_unpaired.txt @ 2:95a632a71951 draft

Uploaded v0.0.6, adds unit test

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:

<tool file="fastq/fastq_paired_unpaired.xml" />

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
v0.0.6 - Record script version when run from Galaxy
       - Added unit test (FASTQ file using Sanger naming)


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://toolshed.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.* test-data/sanger-pairs-*.fastq

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
test-data/sanger-pairs-forward.fastq
test-data/sanger-pairs-interleaved.fastq
test-data/sanger-pairs-mixed.fastq
test-data/sanger-pairs-reverse.fastq
test-data/sanger-pairs-singles.fastq


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.