annotate tools/venn_list/README.rst @ 11:679b6323db03 draft

v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.

Galaxy tool to draw a Venn Diagram with up to 3 sets
====================================================

This tool is copyright 2011-2017 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 the Galaxy and Biopython library
functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
sets, which are then drawn using the R limma package function vennDiagram
(called from Python using rpy).

This tool is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list


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

This should be straightforward, Galaxy should automatically download the tool
and the Python dependencies Biopython and rpy, and the R/Bioconductor package
limma.


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

There are just two files to install:

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

The suggested location is in the Galaxy folder ``tools/plotting`` next to other
graph drawing tools, or a dedicated ``tools/venn_list`` directory.

You will also need to install Biopython 1.54 or later, matplotlib, and
matplotlib_venn - all available via PyPI or Conda,

You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
tool. The suggested location is in the "Graph/Display Data" section. Simply add
the line::

  <tool file="venn_list/venn_list.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 venn_list


History
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.3  - Initial public release.
v0.0.4  - Ignore blank lines when loading IDs from tabular files
v0.0.5  - Explicit Galaxy error handling of return codes
v0.0.6  - Added unit tests.
        - Use reStructuredText for this README file.
        - Adopt standard MIT licence.
        - Updated citation information (Cock et al. 2013).
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
v0.0.7  - Renamed folder and README file.
        - Tool definition now embeds citation information.
v0.0.8  - Reorder XML elements (internal change only).
        - Fixed and improved error handling when rpy is not available.
        - Test output relaxed to cope with more variation in PDF output.
        - Declare Biopython dependency via the Tool Shed.
v0.0.9  - Test with three-way Venn diagram.
        - Includes testing of failure mode.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Tool Shed dependency for rpy and limma (thanks to Björn Grüning).
v0.0.10 - Updated to point at Biopython 1.67 (latest version in Tool Shed).
        - Explicit dependency on ``galaxy_sequence_utils``.
        - Python style updates (internal change only).
v0.0.11 - Use ``<command detect_errors="aggressive">`` (internal change only).
        - Single quote command line arguments (internal change only)
        - Python 3 compatible print function.
        - Capture python script version when run from Galaxy.
v0.0.12 - Internal Python style change.
        - Python 3 compatible exception handling.
v0.1.0  - Now uses Python library matplotlib_venn to draw the diagram
          instead of R's limma via rpy). Contribution from Frederic Sapet.
======= ======================================================================


Developers
==========

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

Development has now moved to a dedicated GitHub repository:
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/venn_list/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/venn_list/
    ...
    $ tar -tzf shed_upload.tar.gz
    tools/venn_list/README.rst
    tools/venn_list/tool_dependencies.xml
    tools/venn_list/venn_list.py
    tools/venn_list/venn_list.xml
    test-data/magic.pdf
    test-data/rhodopsin_proteins.fasta
    test-data/venn_list.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.