Metadata-Version: 2.1
Name: metaMS
Version: 1.0.0
Summary: Data processing, and annotation for metabolomics analysis by low-resolution GC-MS
Home-page: https://gitlab.pnnl.gov/mass-spectrometry/metaMS
Author: Corilo, Yuri
Author-email: corilo@pnnl.gov
License: BSD
Description: # MetaMS
        
        **MetaMS** is a workflow for metabolomics data processing and annotation
        
        ## Current Version
        
        ### `1.0.0`
        
        ### Data input formats
        
        - ANDI NetCDF for GC-MS (.cdf)
        - CoreMS self-containing Hierarchical Data Format (.hdf5)
        - ChemStation Agilent (Ongoing)
        
        ### Data output formats
        
        - Pandas data frame (can be saved using pickle, h5, etc)
        - Text Files (.csv, tab separated .txt, etc)
        - Microsoft Excel (xlsx)
        - JSON for workflow metadata
        - Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
        
        ### Data structure types
        
        - GC-MS
        
        ## Available features
        
        ### Signal Processing
        
        - Baseline detection, subtraction, smoothing 
        - Manual and automatic noise threshold calculation
        - First and second derivatives peak picking methods
        - Peak Area Calculation
        - EIC Chromatogram deconvolution(TODO)
        
        ### Calibration
        
        - Retention Index Linear XXX method 
        
        ### Compound Identification
        
        - Automatic local (SQLite) or external (MongoDB or PostgreSQL) database check, generation, and search
        - Automatic molecular match algorithm with all spectral similarity methods 
        
        ## MetaMS Installation
        
        - PyPi:     
        ```bash
        pip3 install metams
        ```
        
        - From source:
         ```bash
        pip3 install --editable .
        ```
        
        To be able to open chemstation files a installation of pythonnet is needed:
        - Windows: 
            ```bash
            pip3 install pythonnet
            ```
        
        - Mac and Linux:
            ```bash
            brew install mono
            pip3 install pythonnet   
            ```
        
        ## Usage
        
        ```bash
        metaMS dump_json_template MetamsFile.json
        ```
        ```bash
        metaMS dump_corems_json_template CoremsFile.json
        ```
        
         Modify the MetamsFile.json and CoremsFile.json accordingly to your dataset and workflow parameters
        make sure to include CoremsFile.json path inside the MetamsFile.json: "corems_json_path": "path_to_CoremsFile.json" 
        
        ```bash
        metaMS run-gcms-workflow path_to_MetamsFile.json
        ```
        
        ## MetaMS Docker 
        
        A docker image containing the MetaMS command line as the entry point
        
        If you don't have docker installed, the easiest way is to [install docker for desktop](https://hub.docker.com/?overlay=onboarding)
        
        - Pull from Docker Registry:
        
            ```bash
            docker pull corilo/metams:latest
            
            ```
        
        - Build the image from source:
        
            ```bash
            docker build -t metams:latest .
            ```
        - Run Workflow from Container:
        
            $(data_dir) = dir_containing the gcms data, MetamsFile.json and CoremsFile.json
            
            ```bash
            docker run -v $(data_dir):/metaB/data corilo/metams:latest run-gcms-workflow /metaB/data/MetamsFile.json    
            ```
        
        - Getting the parameters templates:
            
            ```bash
            docker run -v $(data_dir):/metaB/data corilo/metams:latest dump_json_template /metaB/data/MetamsFile.json    
            ```
            
            ```bash
            docker run -v $(data_dir):/metaB/data corilo/metams:latest dump_corems_json_template /metaB/data/CoremsFile.json
            ```
            
Platform: UNKNOWN
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
