52 <param name="classes" argument="--classes" type="text" value="None" label="Classes:" help="Write here the the classes to assign to each of the uploaded RAS matrices. Example for two RAS matrices:'cellNormal, cellCancer'. If you uploaded just one matrix, leave default value." />
81 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) both with and without the use of the Reaction Activity Scores (RAS) matrix generated by RAS generator.
82 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
83 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned.
87 - RAS matrix: tab-separated RAS file as returned by RAS generator. It can be a collection of RAS files too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells.
88 - Classes: If multiple RAS matrices are uploaded, then the tool returns a simple file containing for each cell the class it belongs to (cells coming from the same RAS matrix are assigned to the same class). This file is useful in the Flux enrichment analysis tool.