Package: metaMS
Table of ContentsIntroductionMetaMSVersionData InputData OutputData StructureFeaturesCode DocumentationInstallationPyPiExecution:CLIMiniWDLDocker ContainerMetaMSMetaMSis a workflow for metabolomics data processing and annotationCurrent Version2.1.3Data input formatsANDI NetCDF for GC-MS (.cdf)CoreMS self-containing Hierarchical Data Format (.hdf5)ChemStation Agilent (Ongoing)Data output formatsPandas data frame (can be saved using pickle, h5, etc)Text Files (.csv, tab separated .txt, etc)Microsoft Excel (xlsx)JSON for workflow metadataSelf-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributesData structure typesGC-MSAvailable featuresSignal ProcessingBaseline detection, subtraction, smoothingm/z based Chromatogram Peak Deconvolution,Manual and automatic noise threshold calculationFirst and second derivatives peak picking methodsPeak Area CalculationCalibrationRetention Index Linear XXX methodCompound IdentificationAutomatic local (SQLite) or external (MongoDB or PostgreSQL) database check, generation, and searchAutomatic molecular match algorithm with all spectral similarity methodsMetaMS InstallationPyPi:pip3installmetamsFrom source:pip3install--editable.To be able to open chemstation files a installation of pythonnet is needed:Windows:pip3installpythonnetMac and Linux:brewinstallmono
pip3installpythonnetExecutionmetaMSdump_json_templateMetamsFile.jsonmetaMSdump_corems_json_templateCoremsFile.jsonModify 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"metaMSrun-gcms-workflowpath_to_MetamsFile.jsonMiniWDLChange wdl/metams_input.json to specify the data locationChange data/CoremsFile.json to specify the workflow parametersInstall miniWDL:pip3installminiwdlCall:miniwdlrunwdl/metaMS.wdl-iwdl/metams_input.json--verbose--no-cache--copy-input-filesMetaMS Docker ContainerA docker image containing the MetaMS command line as the entry pointIf you don't have docker installed, the easiest way is toinstall docker for desktopPull from Docker Registry:dockerpullcorilo/metams:latestor Build the image from source:dockerbuild-tmetams:latest.Run Workflow from Container:$(data_dir) = full path of directory containing the gcms data, MetamsFile.json and CoremsFile.jsondockerrun-v$(data_dir):/metaB/datacorilo/metams:latestmetaMSrun-gcms-workflow/metaB/data/MetamsFile.jsonGetting the parameters templates:dockerrun-v$(data_dir):/metaB/datacorilo/metams:latestmetaMSdump_json_template/metaB/data/MetamsFile.jsondockerrun-v$(data_dir):/metaB/datacorilo/metams:latestmetaMSdump_corems_json_template/metaB/data/CoremsFile.jsonDisclaimerThis material was prepared as an account of work sponsored by an agency of the
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