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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 :: Text Processing :: Markup :: XML",
            "Topic :: Utilities"
        ],
        "description": "nmrml2isa-qt\n============\n\nA PyQt interface for nmrml2isa parser\n'''''''''''''''''''''''''''''''''''''\n\nOverview\n--------\n\nThis program is a Graphical User Interface for the\n`nmrml2isa <https://github.com/althonos/nmrml2isa>`__ parser. It provides\nan easy-to-use interface to convert nmrML files to an ISA-Tab Study. It\nwas made with Python3 and PyQt5.\n\nInstall\n-------\n\nWith PIP\n~~~~~~~~\n\nIf ``pip`` is present on your system (comes along most of Python install\n/ releases), it can be used to install the program and its dependencies:\n\n.. code:: bash\n\n    pip3 install nmrml2isa-qt\n\nWithout PIP\n~~~~~~~~~~~\n\nOnce dependencies installed, clone the **nmrml2isa-qt** repository to a\nfolder with writing permissions:\n\n.. code:: bash\n\n    git clone git://github.com/althonos/nmrml2isa-qt\n\nAfter that, either run the GUI directly:\n\n.. code:: bash\n\n    python3 run.py\n\nOr install it locally to run with ``nmrmlisa-qt`` command:\n\n.. code:: bash\n\n    cd nmrml2isa-qt && python3 setup.py install\n\nUse\n---\n\nOpen the GUI with the ``nmrml2isa-qt`` command. To simply parse **.nmrML**\nfiles to **ISA**, select the directory containing your files. With\ndefault settings, the program will create the new ISA files in that\nfolder, assuming the folder's name is the study identifier (*MTBSLxxx*\nfor instance for MetaboLights studies). This can be changed by unticking\nthe ``Export result to directory of each study`` box. Once parameters\nare set up, click the ``Convert`` button to start the parser.\n\nMetaboLights\n------------\n\nGenerating a study to upload on MetaboLights requires pieces of\ninformation the parser cannot guess from the mzML file alone. To provide\nmore metadata to your final ISA-Tab files, use the ``Add Metadata``\nbutton to open a new window and update details about your study. Still,\neven with all the required fields filled, **the generated ISA needs to\nbe enhanced after the end of the parsing** (using for instance\n`Metabolight pre-packaged ISA\nCreator <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\n  and to the *investigation* file)\n- Metabolite Assignment Files\n- Study Designs\n\nTODO\n----\n\n-  Either add a ``metabolite assignment file`` field to main window or\n   change the **nmrml2isa** parser behaviour so that it successfully\n   detects metabolite assignment files and add them to the study file.\n\nLicense\n-------\n\nGPLv3",
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        "keywords": "Metabolomics,Mass spectrometry,Imaging Mass Spectrometry,metabolites,ISA Tab,imzML,parsing",
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