mzml2isa for galaxy

This is a Galaxy wrapper for the mzml2isa python package tool.

• Full documentation: http://2isa.readthedocs.io/en/latest/
• Python PyPi package: https://pypi.python.org/pypi/mzml2isa/
• Github code: https://github.com/ISA-tools/mzml2isa

mzml2isa is a program that allows you to convert metabolomic studies in .mzML format to the open ISA-Tab standard supported by the MetaboLights database.

Installation

The recommended installation is by means of the toolshed (https://toolshed.g2.bx.psu.edu/). Dependencies should be installed automatically when using Galaxy version >= 16.10.

The dependencies are dealt with Bioconda. To ensure that Bioconda is working check to make sure the following settings are in the config/galaxy.ini file.

# dependencies before each job runs.
conda_auto_install = True
# Set to True to instruct Galaxy to install Conda from the web automatically
# if it cannot find a local copy and conda_exec is not configured.
conda_auto_init = True

Licence

GNU General Public License v3 (GPLv3)

Changes

v1.1.1+galaxy1

• Fix dependency issues - specifically required "zip"

v1.1.1+galaxy0

• Version bump to mzml2isa 1.1.1
• Galaxy tool python3 compatible (https://github.com/ISA-tools/mzml2isa-galaxy/issues/10)
• Removed functionality to add additional usermeta data for ISA directly via individual Galaxy Tool inputs (deemed unpractical - and is suited for a separate tool). A JSON file can still be used for this functionality
• Highlight tar option more clearly (https://github.com/ISA-tools/mzml2isa-galaxy/pull/5)
• Bug fixed for json handling (https://github.com/ISA-tools/mzml2isa-galaxy/issues/6)
• CI/CD updates

v0.1.0

• For mzml2isa v0.4.24 (For Galaxy-python2 only)