Tool specification file

Tool specification file

MuGVRE has a register of all the tools integrated in the infrastructure. In the database, each tool is defined in terms of input files, arguments, output files and other metadata demanded by MuGVRE to be able to interact with such tool. All this data ought to be provided by the tool developer in a standardized JSON file as defined in the following JSON SCHEMA. Some examples are also offered.


Tool specification schema tool_schema.json (*)
Examples of tool specification jsons tool_schema_examples

(*) The JSON schema details the values each attribute accepts, but if your tool doesn’t fit in any of the contemplated cases, contact us.

Below, the list accepted fields included in the tool definition. This is only a short description, so please, check the whole tool_schema referred above for more information.



Output metadata file

Contains the metadata for the tool’s output files changing in each execution. If results are dynamic or dependent on input metadata, some metadata fields cannot be predefined when specifying the tool in the ‘tool specification file’ (i.e. the BAM ‘assembly’ is dependent on the FASTQ ‘assembly’ used as input). In such cases, the tool should create an additional file called output metadata file containing such metadata fields.


Example of output file metadata output_metadata.json