rpGlobalScore
Tool that reads a collection of rpSBML files (in a tar.xz) and calculates a global score based on a series of weights given by the user
Getting Started
This is a docker galaxy tools, and thus, the docker needs to be built locally where Galaxy is installed.
Input
Required information:
- -input: (string) Path to either tar.xz input collection of rpSBML files or a single rpSBML file.
- -input_format: (string) Format of the input
Advanced options:
- -fba_ceil: (float, default=3.0) FBA ceiling
- -fba_floor: (float, default=0.0) FBA floor
- -thermo_ceil: (float, default=8901.2) Thermodynamics ceiling
- -thermo_floor: (float, default=-7570.2) Thermodynamics floor
- -weight_rp_steps: (float, default=0.0) Number of steps weight
- -max_rp_steps: (integer, default=15) Maximal number of steps (as run in RetroPath2.0)
- -weight_rule_score: (float, default=0.0) Reation rule score weight
- -weight_fba: (float, default=0.699707) FBA weight
- -weight_thermo: (float, default=0.8334961) Pathway thermodynamics weight
- -pathway_id: (string, default=rp_pathway) Name of the heterologous pathway
- -objective_id: (string, default=obj_RP1_sink__restricted_biomass) Name of the heterologous pathway objective function
- -thermo_id: (string, default=dfG_prime_m) Name of the thermodynamics
Output
- output: (string) Path to the output file
Dependencies
Installing
To build the image using the Dockerfile, use the following command:
docker build -t brsynth/rpglobalscore-standalone -f Dockerfile .
Running the tests
To run the test, untar the test.tar.xz file and run the following command:
python run.py -input test/test_rpGlobalScore.tar -input_format tar -output test/test_output.tar
Contributing
Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.
Versioning
v0.1
Authors
License
This project is licensed under the MIT License - see the LICENSE.md file for details
Acknowledgments
- Thomas Duigou
- Joan Hérisson
How to cite rpGlobalScore?