comparison tools/fastq_filter_by_id/README.rst @ 3:e0041942a12d draft default tip

v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license

3:e0041942a12d

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This tool is now obsolete, having been replaced	by a more general version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 2010-2017 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below (MIT licence).

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
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
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
v0.0.5  - Explicit dependency on ``galaxy_sequence_utils``.
        - Citation information (Cock et al. 2013).
        - Explicitly record version via ``<version_command>``.
        - Use ``format_source``/``metadata_source`` idiom for output format.
        - Use standard MIT license (was previously using the MIT/BSD style
          Biopython Licence Agreement).
======= ======================================================================


Developers
==========

This script and other tools for filtering FASTA, FASTQ and SFF files were
initially developed on the following hg branches:
http://bitbucket.org/peterjc/galaxy-central/src/tools
http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter

It is now under GitHub https://github.com/peterjc/pico_galaxy/

For pushing a release to the test or main "Galaxy Tool Shed", use the following
Planemo commands (which requires you have set your Tool Shed access details in
``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

    $ planemo shed_update -t testtoolshed --check_diff tools/fastq_filter_by_id/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff tools/fastq_filter_by_id/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only tools/fastq_filter_by_id/
    ...
    $ tar -tzf shed_upload.tar.gz
    tools/fastq_filter_by_id/README.rst
    tools/fastq_filter_by_id/fastq_filter_by_id.py
    tools/fastq_filter_by_id/fastq_filter_by_id.xml
    tools/fastq_filter_by_id/tool_dependencies.xml
    test-data/empty_file.dat
    test-data/sanger-pairs-mixed.fastq
    test-data/sanger-pairs-names.tabular


Licence (MIT)
=============

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.