Galaxy tool wrapper for MetFrag.
Website: http://c-ruttkies.github.io/MetFrag
Source code: https://github.com/c-ruttkies/MetFrag
- MetFrag tool - v2.4.5+galaxy3
- MetFrag Vis tool - v2.4.5+galaxy0
(Using MetFrag v2.4.5)
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
The list of suspects is an aggregated list of in silico predicted MS/MS spectra of natural products from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php). The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs.
- Jordi Capellades ([email protected]) - Universitat Rovira i Virgili (Tarragona, Spain)
- Julien Saint-Vanne ([email protected]) - ABiMS (France)
- Tom Lawson ([email protected]) - University of Birmingham (UK)
- Kristian Peters ([email protected]) - IPB Halle (Germany)
- Payam Emami ([email protected]) - Uppsala Universitet (Sweden)
- Steffen Neumann ([email protected]) - IPB Halle (Germany)
- Christoph Ruttkies ([email protected]) - IPB Halle (Germany)
- Ralf J. M. Weber ([email protected]) - University of Birmingham (UK)
- 2nd July 2020
- NEW TOOL "MetFrag Vis" - 2.4.5+galaxy0 released
- Thanks Kristian Peters!
- Enhanced visualisation of MetFrag results
- Metfrag tool - 2.4.5+galaxy3 released
- Option added to include all fragment peaks in output
- Additional meta columns added for output (if available) e.g. retention time
- Provide adducts at tool level as well as MSP level
- Version 2.4.5+galaxy2
- Change owner to computational-metabolomics
- Update tests output based on updates of external compound databases
- Version 2.4.5+galaxy1
- Update based on IUC guidlines
- Version 2.4.5+galaxy0.1.13
- Submitted to test toolshed (8:9a3019c609d9)
- Improved reporting of adducts
- Removed print output of settings that might reveal sensitive details regarding the database
- Added missing inchikey column to metchem output
- Version 2.4.5+galaxy0.1.12
- Submitted to test toolshed (7:0b3816a7a14b)
- Allow metchem database to be configured via a config.ini file (allows more flexibility)
- Version 2.4.5+galaxy0.1.11
- Submitted to test toolshed (6:ceb9bd68f6bc)
- Update to MetFrag version 2.4.5
- Boolean for default suspect list fixed
- Check for no results added
- Doc updates
- Version 2.4.2+galaxy0.1.10
- Submitted to test toolshed (5:c53ed894d736)
- Add default option for suspectlist (so user does not need to upload the GNPS list)
- Changed "Minimum percentage of explain peaks" argument to float
- Added "skip invalid adducts" option
- Updated unit-tests
- Check for empty input file added
- Version 2.4.2+galaxy0.1.9
- Submitted to test toolshed (4:eb581a101672)
- Bug fix for neutral mass calculation (Introduced from 0.1.3)
- Additional adduct forms for negative added
- Version system changed to IUC style (TOOL_VERSION+GALAXY_TOOL_VERSION)
- Memory regex check added to stdio - should now repeat at higher memory if low memory error found
- Update unit-tests to use RP022611 MassBank data (Glucose)
- Version 0.1.8:
- removed quotes for output columns (previously double quotes " were being added for inchikeys and scores causing problems for downstream processing.
- Version 0.1.7:
- Bug Fix for ID tracking
- Bug Fix for skipping final MSP spectra if two empty lines not present
- Version 0.1.6:
- Bug Fix for when NoExplPeaks is zero
- Version 0.1.5:
- Fix to add MetChem command line param
- Added auto select for MSP schema
- Added unit test for suspect list
- Version 0.1.4:
- added UNPD InCHIkey database to be used for automated testing
- acknowledge additional contributors
- Version 0.1.3:
- merge with the latest PhenoMeNal develop version of the module, based on https://github.com/korseby/container-msnbase
- merge with changes of Julien Saint-Vanne
Released under the GNU General Public License v3.0 (see LICENSE file)