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

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This tool is now obsolete, having been replaced	by a more general version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.