Metadata-Version: 1.1
Name: nmrml2isa-qt
Version: 0.1.0
Summary: A PyQt interface for nmrml2isa parser.
Home-page: https://github.com/althonos/nmrzml2isa-qt
Author: Martin Larralde
Author-email: martin.larralde@ens-cachan.fr
License: GPLv3
Description: nmrml2isa-qt
        ============
        
        A PyQt interface for nmrml2isa parser
        '''''''''''''''''''''''''''''''''''''
        
        Overview
        --------
        
        This program is a Graphical User Interface for the
        `nmrml2isa <https://github.com/althonos/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
        -------
        
        With PIP
        ~~~~~~~~
        
        If ``pip`` is present on your system (comes along most of Python install
        / releases), it can be used to install the program and its dependencies:
        
        .. code:: bash
        
            pip3 install nmrml2isa-qt
        
        Without PIP
        ~~~~~~~~~~~
        
        Once dependencies installed, clone the **nmrml2isa-qt** repository to a
        folder with writing permissions:
        
        .. code:: bash
        
            git clone git://github.com/althonos/nmrml2isa-qt
        
        After that, either run the GUI directly:
        
        .. code:: bash
        
            python3 run.py
        
        Or install it locally to run with ``nmrmlisa-qt`` command:
        
        .. code:: bash
        
            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 <http://www.ebi.ac.uk/metabolights/>`__ 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
        
        
Keywords: Metabolomics,Mass spectrometry,Imaging Mass Spectrometry,metabolites,ISA Tab,imzML,parsing
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Text Processing :: Markup :: XML
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Classifier: Operating System :: OS Independent
