{
    "id": "gmx_rms",
    "description": "Wrapper of the GROMACS rms module for performing a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.",
    "arguments": [
        {
            "id": "config",
            "required": false,
            "description": "Configuration file for the gmx_rms tool",
            "filetype": "input",
            "sample": "https:\/\/raw.githubusercontent.com\/bioexcel\/biobb_analysis\/master\/biobb_analysis\/test\/data\/config\/config_gmx_rms.json",
            "formats": [
                ".*\\.json$",
                ".*\\.yml$",
                ".*\\.yaml$"
            ]
        },
        {
            "id": "input_structure_path",
            "required": true,
            "description": "Path to the input structure file",
            "filetype": "input",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_analysis\/raw\/master\/biobb_analysis\/test\/data\/gromacs\/topology.tpr",
            "formats": [
                ".*\\.tpr$",
                ".*\\.gro$",
                ".*\\.g96$",
                ".*\\.pdb$",
                ".*\\.brk$",
                ".*\\.ent$"
            ]
        },
        {
            "id": "input_traj_path",
            "required": true,
            "description": "Path to the GROMACS trajectory file",
            "filetype": "input",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_analysis\/raw\/master\/biobb_analysis\/test\/data\/gromacs\/trajectory.trr",
            "formats": [
                ".*\\.xtc$",
                ".*\\.trr$",
                ".*\\.cpt$",
                ".*\\.gro$",
                ".*\\.g96$",
                ".*\\.pdb$",
                ".*\\.tng$"
            ]
        },
        {
            "id": "input_index_path",
            "required": false,
            "description": "Path to the GROMACS index file",
            "filetype": "input",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_analysis\/raw\/master\/biobb_analysis\/test\/data\/gromacs\/index.ndx",
            "formats": [
                ".*\\.ndx$"
            ]
        },
        {
            "id": "output_xvg_path",
            "required": true,
            "description": "Path to the XVG output file",
            "filetype": "output",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_analysis\/raw\/master\/biobb_analysis\/test\/reference\/gromacs\/ref_rms.xvg",
            "formats": [
                ".*\\.xvg$"
            ]
        }
    ]
}