nmrml2isa-qt 0.1.0

Overview

This program is a Graphical User Interface for the nmrml2isa parser. It provides an easy-to-use interface to convert nmrML files to an ISA-Tab Study. It was made with Python3 and PyQt5.

Install

pip3 install nmrml2isa-qt

git clone git://github.com/althonos/nmrml2isa-qt

python3 run.py

cd nmrml2isa-qt && python3 setup.py install

Use

Open the GUI with the nmrml2isa-qt command. To simply parse .nmrML 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 the Export result to directory of each study box. Once parameters are set up, click the Convert button to start the parser.

MetaboLights

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 Add Metadata 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

TODO

• Either add a metabolite assignment file field to main window or change the nmrml2isa parser behaviour so that it successfully detects metabolite assignment files and add them to the study file.

License

GPLv3