A PyQt interface for mzml2isa parser - imzML edition.
This program is a Graphical User Interface for the mzml2isa parser. It provides an easy-to-use interface to convert mzML files to an ISA-Tab Study. It was made with Python3 and PyQt5.
pip is present on your system (comes along most of Python install
/ releases), it can be used to install the program and its dependencies:
pip3 install imzml2isa-qt
Once dependencies installed, clone the imzml2isa-qt repository to a folder with writing permissions:
git clone git://github.com/althonos/imzml2isa-qt
After that, either run the GUI directly:
Or install it locally to run with
cd imzml2isa-qt && python3 setup.py install
Open the GUI with the
imzml2isa-qt command. To simply parse .imzML
files to ISA, select the directory containing your files. With
default settings, the program will create the new ISA files in that
folder, assuming the folder's name is the study identifier (MTBSLxxx
for instance for MetaboLights studies). This can be changed by unticking
Export result to directory of each study box. Once parameters
are set up, click the
Convert button to start the parser.
Generating a study to upload on MetaboLights requires pieces of
information the parser cannot guess from the mzML file alone. To provide
more metadata to your final ISA-Tab files, use the
button to open a new window and update details about your study. Still,
even with all the required fields filled, the generated ISA needs to
be enhanced after the end of the parsing (using for instance
Metabolight pre-packaged ISA
Creator to add missing fields).
Missing information required for MetaboLights upload are at the moment: - Study Factors (sample dependent, must be added to the study file
and to the investigation file)
- Metabolite Assignment Files
- Study Designs
- Either add a
metabolite assignment filefield to main window or change the mzml2isa parser behaviour so that it successfully detects metabolite assignment files and add them to the study file.