view tools/seq_filter_by_id/README.rst @ 7:fb1313d79396 draft

Uploaded v0.2.5, ignore blank names in tabular files (based on contribution from Gildas Le Corguille)

Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID
=========================================================

This tool is copyright 2010-2015 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

This tool is a short Python script (using both Biopython library functions)
which divides a FASTA, FASTQ, or 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.

This tool is available from the Galaxy Tool Shed at:

* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id

See also sister tools:

* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping


Automated Installation
======================

This should be straightforward using the Galaxy Tool Shed, which should be
able to automatically install the dependency on Biopython, and then install
this tool and run its unit tests.


Manual Installation
===================

There are just two files to install to use this tool from within Galaxy:

* ``seq_filter_by_id.py`` (the Python script)
* ``seq_filter_by_id.xml`` (the Galaxy tool definition)

The suggested location is a dedicated ``tools/seq_filter_by_id`` folder.

You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
tool. One suggested location is in the filters section. Simply add the line::

    <tool file="seq_filter_by_id/seq_filter_by_id.xml" />

If you wish to run the unit tests, also move/copy the ``test-data/`` files
under Galaxy's ``test-data/`` folder. Then::

    $ ./run_tests.sh -id seq_filter_by_id

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


History
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.1  - Initial version, combining three separate scripts for each file format.
v0.0.4  - Record script version when run from Galaxy.
        - Faster FASTA code which preserves the original line wrapping.
        - Basic unit test included.
v0.0.5  - Check for errors using Python script's return code.
        - Cope with malformed FASTA entries without an identifier.
v0.0.6  - Link to Tool Shed added to help text and this documentation.
        - Automated installation of the Biopython dependency.
        - Use reStructuredText for this README file.
        - Adopt standard MIT License.
        - Updated citation information (Cock et al. 2013).
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
        - Renamed folder and adopted README.rst naming.
v0.0.7  - Correct automated dependency definition.
v0.0.8  - Simplified XML to apply input format to output data.
v0.2.0  - Can supply ID list as a text parameter (instead of in a file)
        - Using ``optparse`` for the Python command line API.
        - Advanced option to ignore paired read suffices.
        - Updated dependencies to use Biopython 1.64.
v0.2.1  - Use Biopython instead of Galaxy for FASTQ handling.
        - Tool definition now embeds citation information.
        - Include input dataset name in output dataset names.
        - If white space is found in the requested tabular field then only
          the first word is used as the identifier (with a warning to stderr).
v0.2.2  - Use the ``format_source=...`` tag.
        - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.2.3  - Ignore blank lines in ID file (contributed by Gildas Le Corguillé).
        - Defensive quoting of filenames etc in the command definition
          (internal change only).
v0.2.4  - Corrected error message wording.
v0.2.5  - Ignore empty names, common in R output (Gildas Le Corguillé).
======= ======================================================================


Developers
==========

This script and related tools were initially developed on the following hg branches:
http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools

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/seq_filter_by_id/ -m "New release"
    ...

or::

    $ planemo shed_update -t toolshed --check_diff tools/seq_filter_by_id/ -m "New release"
    ...

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

    $ planemo shed_upload --tar_only tools/seq_filter_by_id/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/empty_file.dat
    test-data/k12_hypothetical.fasta
    test-data/k12_hypothetical.tabular
    test-data/k12_hypothetical_alt.tabular
    test-data/k12_ten_proteins.fasta
    test-data/sanger-pairs-mixed.fastq
    test-data/sanger-pairs-names.tabular
    test-data/sanger-sample.fastq
    tools/seq_filter_by_id/README.rst
    tools/seq_filter_by_id/seq_filter_by_id.py
    tools/seq_filter_by_id/seq_filter_by_id.xml
    tools/seq_filter_by_id/tool_dependencies.xml


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.