Metadata-Version: 2.1
Name: mzml2isa
Version: 1.0.1
Summary: mzML file parser and converter to ISA-Tab
Home-page: https://github.com/ISA-tools/mzml2isa
Author: Tom Lawson, Martin Larralde
Author-email: tnl495@bham.ac.uk
License: GPLv3
Project-URL: Bug Reports, https://github.com/ISA-tools/mzml2isa/issues
Project-URL: Documentation, http://2isa.readthedocs.io/en/latest/mzml2isa/
Project-URL: Changelog, https://github.com/ISA-tools/mzml2isa/blob/master/CHANGELOG.md
Description: ``mzml2isa``
        ============
        
        Extract metadata from `mzML` and `imzML` files and write them to an ISA-Tab document.
        
        |Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |DOI| |Paper|
        
        
        Overview
        --------
        
        mzml2isa is a Python3 program that can automatically generate ISA-Tab document
        structure metadata files from raw XML metabolomics data files (mzML open access data format).
        The mzml2isa tool provides the backbone of ISA-Tab metabolomics study which can
        then be edited with an ISA editing tool, ISAcreator (see `MetaboLights pre-packaged
        ISA Creator <http://www.ebi.ac.uk/metabolights/>`__)
        
        **Features**:
          * Extract meta information from `mzML` files and stores it as a Python dictionary or
            serialize it into a JSON formatted document.
          * Create an ISA-Tab file structure with relevant meta information filled in.
          * Add additional metadata that cannot be parsed from mzML files to the
            ISA-Tab files through a JSON formatted dictionnary or an XLS file.
        
        
        Install
        -------
        
        See the `Installation page <http://2isa.readthedocs.io/en/latest/mzml2isa/install.html>`__ of
        the `online documentation <http://2isa.readthedocs.io/en/latest/mzml2isa/index.html>`__.
        
        
        Usage
        -----
        
        CLI
        '''
        
        .. code:: bash
        
            mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s name_of_study
        
        Python Module
        '''''''''''''
        
        See the `Usage page <http://2isa.readthedocs.io/en/latest/mzml2isa/usage.html>`__ and
        the `Examples page <http://2isa.readthedocs.io/en/latest/mzml2isa/examples.html>`__ for more
        information.
        
        
        Metabolights
        ------------
        
        To download some real data from
        `MetaboLights <http://www.ebi.ac.uk/metabolights/>`__ studies to test
        the converter with, run
        
        .. code:: bash
        
            python scripts/metabolights-dl.py <size>
        
        from inside the repository, where *size* is the maximum size in GiB you
        can allocate to download files. The script will download the files to
        the ``example_files/metabolight``\ s folder and then run mzml2isa on
        those files..
        
        If you use a \*NIX machine with **curlftpfs** and **bash** available,
        you can also run
        
        .. code:: bash
        
            scripts/metabolights.sh
        
        to mount the database to the example directory and start converting mzML
        studies.
        
        Workflow
        --------
        
        .. figure:: static/mzml2isa.png
           :alt: workflow
        
        .. |Build Status (Travis)| image:: https://img.shields.io/travis/ISA-tools/mzml2isa.svg?style=flat&maxAge=3600&label=Travis-CI
           :target: https://travis-ci.org/ISA-tools/mzml2isa
        
        .. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/Tomnl/mzml2isa.svg?style=flat&maxAge=3600&label=AppVeyor
           :target: https://ci.appveyor.com/project/Tomnl/mzml2isa
        
        .. |Py versions| image:: https://img.shields.io/pypi/pyversions/mzml2isa.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/mzml2isa/
        
        .. |Version| image:: https://img.shields.io/pypi/v/mzml2isa.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/mzml2isa/
        
        .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
           :target: https://github.com/ISA-tools/mzml2isa
        
        .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
           :target: http://bioconda.github.io/recipes/mzml2isa/README.html
        
        .. |License| image:: https://img.shields.io/pypi/l/mzml2isa.svg?style=flat&maxAge=3600
           :target: https://www.gnu.org/licenses/gpl-3.0.html
        
        .. |RTD doc| image:: https://img.shields.io/readthedocs/2isa.svg?style=flat&maxAge=3600
           :target: https://2isa.readthedocs.io/en/latest/mzml2isa/
        
        .. |DOI| image:: https://zenodo.org/badge/37276823.svg
           :target: https://zenodo.org/badge/latestdoi/37276823
        
        .. |Paper| image:: https://img.shields.io/badge/paper-Bioinformatics-teal.svg?style=flat&maxAge=3600
           :target: https://academic.oup.com/bioinformatics/article/33/16/2598/3204983
        
Keywords: metabolomics,mass spectrometry,metabolites,ISA Tab,mzML,parser
Platform: any
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Text Processing :: Markup :: XML
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Utilities
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*
Provides-Extra: pb
