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        "author": "Martin Larralde",
        "author_email": "martin.larralde@ens-cachan.fr",
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        "classifiers": [
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator",
            "Topic :: Text Processing :: Markup :: XML",
            "Topic :: Utilities"
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        "description": "# mzml2isa-qt\n#####A PyQt interface for mzml2isa parser.\n\n## Overview\nThis program is a Graphical User Interface for the [mzml2isa](https://github.com/ISA-tools/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\n\n## Install\n\n### With PIP\nIf `pip` is present on your system (comes along most of Python install / releases), it can be used to install the program and its dependencies:\n```bash\npip3 install mzml2isa-qt\n```\n\n### Without PIP\nOnce dependencies installed, clone the **mzml2isa-qt** repository to a folder with writing permissions:\n```bash\ngit clone git://github.com/ISA-tools/mzml2isa-qt\n```\n\nAfter that, either run the GUI directly: \n```bash\npython3 run.py\n```\n\nOr install it locally to run with `mzmlisa-qt` command:\n```bash\ncd mzml2isa-qt && python3 setup.py install\n```\n\n## Use\nOpen the GUI with the `mzml2isa-qt` command. To simply parse **.mzML** 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.\n\n## MetaboLights\nGenerating 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](http://www.ebi.ac.uk/metabolights/) to add missing fields).\n\nMissing information required for MetaboLights upload are at the moment:\n* Study Factors (sample dependent, must be added to the _study_ file and to the _investigation_ file)\n* Metabolite Assignment Files\n* Study Designs\n\n## TODO\n* Either add a `metabolite assignment file` field to main window or change the **mzml2isa** parser behaviour so that it successfully detects metabolite assignment files and add them to the study file.\n\n## License\nGPLv3\n",
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