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Repository 'sff_filter_by_id'
http://toolshed.g2.bx.psu.edu/view/peterjc/sff_filter_by_id
unrestricted
DEPRECATED
This release is to DEPRECATE the tool. The only change is that it is now hidden from display on the left hand side (but can still be used for existing workflows or history entries).

This and the two related tools have been replaced by a single combined tool to filter FASTA, FASTQ or SFF files.
1:9cd3591f6afa
peterjc
True
171

Repository README files - may contain important installation or license information

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This tool is now obsolete, having been replaced by a more general version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 SFF 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 Biopython library functions) which
divides an SFF 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:

* sff_filter_by_id.py (the Python script)
* sff_filter_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 next to the sff_extractor.xml entry. Simply
add the line:

<tool file="filters/sff_filter_by_id.xml" />

You will also need to install Biopython 1.54 or later. That's it.


History
=======

v0.0.1 - Initial version
v0.0.2 - 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 sff_filter_by_id.tar.gz tools/filters/sff_filter_by_id.*

Check this worked:

$ tar -tzf sff_filter_by_id.tar.gz
filter/sff_filter_by_id.py
filter/sff_filter_by_id.txt
filter/sff_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.

Contents of this repository

Name Description Version
Filter SFF by ID from a tabular file 0.0.2

Automated tool test results

Time tested: 2014-04-23 15:10:59
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 13123:e6876f691854
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: sff_filter_by_id
Tool version: 0.0.2
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/sff_filter_by_id/sff_filter_by_id/0.0.2
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for sff_filter_by_id.

Categories
Sequence Analysis