{
  "id": "http://multiscalegenomics.eu/tool-schema",
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "object",
  "title": "MuG tool definition schema",
  "description": "Specification of MuG tools as required for VRE",
  "properties": {
    "_id": {
      "type": "string"
    },
    "name": {
      "type": "string"
    },
    "title": {
      "type": "string",
      "default": "null"
    },
    "short_description": {
      "type": "string",
      "default": "null"
    },
    "long_description": {
      "type": "string",
      "default": "null"
    },
    "url": {
      "type": "string"
    },
    "publication": {
      "type": "string"
    },
    "owner": {
      "type": "object",
      "properties": {
        "institution": {
          "type": "string"
        },
        "author": {
          "type": "string"
        },
        "contact": {
          "type": "string"
        },
        "url": {
          "type": "string"
        }
      },
      "required": [
        "author",
        "institution",
        "contact"
      ],
      "additionalProperties": false
    },
    "keywords": {
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "chromatin",
          "dynamics",
          "visualization",
          "hi-C",
          "epigenetics",
          "nucleosome",
          "modeling",
          "next gen sequencing",
          "interaction",
          "rna",
          "dna",
          "protein",
          "sequence",
          "structure",
          "other"
        ]
      },
      "default": "other"
    },
    "keywords_tool": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "default": "other"
    },
    "infrastructure": {
      "type": "object",
      "properties": {
        "executable": {
          "type": "string"
        },
        "cpus": {
          "type": "integer",
          "minimum": 1,
          "maximum": 12,
          "default": 1
        },
        "memory": {
          "type": "number",
          "minimum": 0,
          "maximum": 24,
          "default": 0
        },
        "wallTime": {
          "type": "integer",
          "minimum": 5,
          "maximum": 1440,
          "default": 1440
        },
        "clouds": {
          "type": "object",
          "properties": {
            "mug-bsc": {
              "$ref": "#/definitions/cloud"
            },
            "mug-irb": {
              "$ref": "#/definitions/cloud"
            },
            "mug-ebi": {
              "$ref": "#/definitions/cloud"
            }
          },
          "additionalProperties": false
        }
      }
    },
    "has_custom_viewer": {
      "type": "boolean",
      "default": true
    },
    "input_files": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "name": {
            "type": "string"
          },
          "description": {
            "type": "string"
          },
          "help": {
            "type": "string",
            "default": null
          },
          "file_type": {
            "type": "array",
            "items": {
              "type": "string",
              "enum": [
                "null",
                "AMB",
                "ANN",
                "BAI",
                "BAM",
                "BB",
                "BED",
                "BEDGRAPH",
                "BT2",
                "BW",
                "BWT",
                "CPT",
                "CSV",
                "DCD",
                "FASTA",
                "FASTQ",
                "GEM",
                "GFF",
                "GFF3",
                "GTF",
                "HDF5",
                "IDX",
                "JSON",
                "LIF",
                "MDCRD",
                "NETCDF",
                "PAC",
                "PARMTOP",
                "PDB",
                "PDF",
                "PICKLE",
                "PNG",
                "RDATA",
                "RST",
                "SA",
                "TAR",
                "TBI",
                "TIFF",
                "TOP",
                "TPR",
                "TSV",
                "TXT",
                "VCF",
                "WIG",
                "XTC"
              ]
            }
          },
          "data_type": {
            "type": "array",
            "items": {
              "type": "string",
              "enum": [
                "chromatin_3dmodel",
                "chromatin_3dmodel_ensemble",
                "chromatin_compartments",
                "chromatin_tads",
                "chromatin_traj",
                "configuration_file",
                "data_atac_seq",
                "data_chip_seq",
                "data_chic",
                "data_dna_methylation",
                "data_fish",
                "data_mnase_seq",
                "data_rna_seq",
                "data_wgbs",
                "docking_ranking",
                "hic_biases",
                "hic_contacts_coverage",
                "hic_contacts_differential",
                "hic_contacts_matrix",
                "hic_contacts_peaks",
                "hic_directionality",
                "hic_reads",
                "hic_sequences",
                "hic_tads_scale",
                "md_restart",
                "na_md_atom_traj_coords",
                "na_md_atom_traj_top",
                "na_md_cg_traj",
                "na_structure",
                "na_traj",
                "na_traj_coords",
                "na_traj_top",
                "nucleosome_dynamics",
                "nucleosome_free_regions",
                "nucleosome_gene_phasing",
                "nucleosome_positioning",
                "nucleosome_stiffness",
                "prot_dna_specificity",
                "prot_dna_structure",
                "prot_structure",
                "chic_matrix",
                "pchic_matrix",
                "pchic_scores",
                "pchAS",
                "sequence_annotation",
                "sequence_dna",
                "sequence_cdna",
                "sequence_genomic",
                "sequence_mapping_index_bowtie",
                "sequence_mapping_index_bwa",
                "sequence_mapping_index_gem",
                "sequence_mapping_index_kallisto",
                "sequence_prot",
                "sequence_rna",
                "structure",
                "tool_intermediate_file",
                "tool_statistics",
                "tss_classification_by_nucleosomes"
              ]
            }
          },
          "required": {
            "type": "boolean",
            "default": true
          },
          "allow_multiple": {
            "type": "boolean",
            "default": false
          }
        },
        "required": [
          "name",
          "description",
          "file_type",
          "data_type",
          "required",
          "allow_multiple"
        ]
      }
    },
    "input_files_public_dir": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "name": {
            "type": "string"
          },
          "description": {
            "type": "string"
          },
          "help": {
            "type": "string",
            "default": null
          },
          "type": {
            "type": "string",
            "enum": [
              "integer",
              "number",
              "string",
              "enum",
              "enum_multiple",
              "boolean",
              "hidden"
            ]
          },
          "default": {
            "type": ["integer", "string", "boolean", "number", "array"],
            "default": "null"
          },
          "value": {
            "type": ["integer", "string", "boolean", "number", "array"],
            "default": "null"
          },
          "enum_items": {
            "type": "object",
            "properties": {
              "name": {
                "type": "array"
              },
              "description": {
                "type": "array"
              }
            },
            "required": [
              "name"
            ],
            "additionalProperties": false
          },
          "file_type": {
            "type": "array",
            "items": {
              "type": "string",
              "enum": [
                "null",
                "AMB",
                "ANN",
                "BAI",
                "BAM",
                "BB",
                "BED",
                "BEDGRAPH",
                "BT2",
                "BW",
                "BWT",
                "CPT",
                "CSV",
                "DCD",
                "FASTA",
                "FASTQ",
                "GEM",
                "GFF",
                "GFF3",
                "GTF",
                "HDF5",
                "IDX",
                "JSON",
                "LIF",
                "MDCRD",
                "NETCDF",
                "PAC",
                "PARMTOP",
                "PDB",
                "PDF",
                "PICKLE",
                "PNG",
                "RDATA",
                "RST",
                "SA",
                "TAR",
                "TBI",
                "TIFF",
                "TOP",
                "TPR",
                "TSV",
                "TXT",
                "VCF",
                "WIG",
                "XTC"
              ]
            }
          },
          "data_type": {
            "type": "array",
            "items": {
              "type": "string",
              "enum": [
                "chromatin_3dmodel",
                "chromatin_3dmodel_ensemble",
                "chromatin_compartments",
                "chromatin_tads",
                "chromatin_traj",
                "configuration_file",
                "data_atac_seq",
                "data_chip_seq",
                "data_chic",
                "data_dna_methylation",
                "data_fish",
                "data_mnase_seq",
                "data_rna_seq",
                "data_wgbs",
                "docking_ranking",
                "hic_biases",
                "hic_contacts_coverage",
                "hic_contacts_differential",
                "hic_contacts_matrix",
                "hic_contacts_peaks",
                "hic_directionality",
                "hic_reads",
                "hic_sequences",
                "hic_tads_scale",
                "md_restart",
                "na_md_atom_traj_coords",
                "na_md_atom_traj_top",
                "na_md_cg_traj",
                "na_structure",
                "na_traj",
                "na_traj_coords",
                "na_traj_top",
                "nucleosome_dynamics",
                "nucleosome_free_regions",
                "nucleosome_gene_phasing",
                "nucleosome_positioning",
                "nucleosome_stiffness",
                "prot_dna_specificity",
                "prot_dna_structure",
                "prot_structure",
                "chic_matrix",
                "pchic_matrix",
                "pchic_scores",
                "pchAS",
                "sequence_annotation",
                "sequence_dna",
                "sequence_cdna",
                "sequence_genomic",
                "sequence_mapping_index_bowtie",
                "sequence_mapping_index_bwa",
                "sequence_mapping_index_gem",
                "sequence_mapping_index_kallisto",
                "sequence_prot",
                "sequence_rna",
                "structure",
                "tool_intermediate_file",
                "tool_statistics",
                "tss_classification_by_nucleosomes"
              ]
            }
          },
          "required": {
            "type": "boolean",
            "default": true
          },
          "allow_multiple": {
            "type": "boolean",
            "default": false
          }
        },
        "additionalProperties": false
      }
    },
    "input_files_combinations": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "description": {
            "type": "string"
          },
          "input_files": {
            "type": "array",
            "items": {
              "type": "string"
            }
          }
        },
        "required": [
          "description",
          "input_files"
        ]
      }
    },
    "arguments": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "name": {
            "type": "string"
          },
          "description": {
            "type": "string"
          },
          "help": {
            "type": "string",
            "default": null
          },
          "type": {
            "type": "string",
            "enum": [
              "integer",
              "number",
              "string",
              "enum",
              "enum_multiple",
              "boolean",
              "hidden"
            ]
          },
          "default": {
            "type": ["integer", "string", "boolean", "number", "array"],
            "default": "null"
          },
          "value": {
            "type": ["integer", "string", "boolean", "number", "array"],
            "default": "null"
          },
          "enum_items": {
            "type": "object",
            "properties": {
              "name": {
                "type": "array"
              },
              "description": {
                "type": "array"
              }
            },
            "required": [
              "name"
            ],
            "additionalProperties": false
          },
          "maximum": {
            "type": "integer"
          },
          "minimum": {
            "type": "integer"
          },
          "required": {
            "type": "boolean",
            "default": true
          },
          "allow_multiple": {
            "type": "boolean",
            "default": false
          }
        },
        "additionalProperties": false,
        "required": [
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          "description",
          "type"
        ]
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    },
    "output_files": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "name": {
            "type": "string"
          },
          "required": {
            "type": "boolean",
            "default": true
          },
          "allow_multiple": {
            "type": "boolean",
            "default": false
          },
          "file": {
            "type": "object",
            "properties": {
              "file_type": {
                "type": "string",
                "enum": [
                  "null",
                  "AMB",
                  "ANN",
                  "BAI",
                  "BAM",
                  "BB",
                  "BED",
                  "BEDGRAPH",
                  "BT2",
                  "BW",
                  "BWT",
                  "CPT",
                  "CSV",
                  "DCD",
                  "FASTA",
                  "FASTQ",
                  "GEM",
                  "GFF",
                  "GFF3",
                  "GTF",
                  "HDF5",
                  "IDX",
                  "JSON",
                  "LIF",
                  "MDCRD",
                  "NETCDF",
                  "PAC",
                  "PARMTOP",
                  "PDB",
                  "PDF",
                  "PICKLE",
                  "PNG",
                  "RDATA",
                  "RST",
                  "SA",
                  "TAR",
                  "TBI",
                  "TIFF",
                  "TOP",
                  "TPR",
                  "TSV",
                  "TXT",
                  "VCF",
                  "WIG",
                  "XTC"
                ]
              },
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                "type": "string",
                "enum": [
                  "chromatin_3dmodel",
                  "chromatin_3dmodel_ensemble",
                  "chromatin_compartments",
                  "chromatin_tads",
                  "chromatin_traj",
                  "configuration_file",
                  "data_atac_seq",
                  "data_chip_seq",
                  "data_chic",
                  "data_dna_methylation",
                  "data_fish",
                  "data_mnase_seq",
                  "data_rna_seq",
                  "data_wgbs",
                  "docking_ranking",
                  "hic_biases",
                  "hic_contacts_coverage",
                  "hic_contacts_differential",
                  "hic_contacts_matrix",
                  "hic_contacts_peaks",
                  "hic_directionality",
                  "hic_reads",
                  "hic_sequences",
                  "hic_tads_scale",
                  "md_restart",
                  "na_md_atom_traj_coords",
                  "na_md_atom_traj_top",
                  "na_md_cg_traj",
                  "na_structure",
                  "na_traj",
                  "na_traj_coords",
                  "na_traj_top",
                  "nucleosome_dynamics",
                  "nucleosome_free_regions",
                  "nucleosome_gene_phasing",
                  "nucleosome_positioning",
                  "nucleosome_stiffness",
                  "prot_dna_specificity",
                  "prot_dna_structure",
                  "prot_structure",
                  "chic_matrix",
                  "pchic_matrix",
                  "pchic_scores",
                  "pchAS",
                  "sequence_annotation",
                  "sequence_dna",
                  "sequence_cdna",
                  "sequence_genomic",
                  "sequence_mapping_index_bowtie",
                  "sequence_mapping_index_bwa",
                  "sequence_mapping_index_gem",
                  "sequence_mapping_index_kallisto",
                  "sequence_prot",
                  "sequence_rna",
                  "structure",
                  "tool_intermediate_file",
                  "tool_statistics",
                  "tss_classification_by_nucleosomes"
                ]
              },
              "file_path": {
                "type": "string"
              },
              "compressed": {
                "type": "string",
                "enum": [
                  "null",
                  "gzip",
                  "zip"
                ]
              },
              "taxon_id": {
                "type": "integer"
              },
              "source_id": {
                "type": "array",
                "items": {
                  "type": "string"
                }
              },
              "meta_data": {
                "type": "object",
                "properties": {
                  "description": {
                    "type": "string"
                  },
                  "tool": {
                    "type": "string"
                  },
                  "assembly": {
                    "type": "string"
                  },
                  "visible": {
                    "type": "boolean",
                    "default": true
                  }
                },
                "required": [
                  "description",
                  "visible"
                ]
              }
            },
            "required": [
              "file_type",
              "data_type",
              "meta_data"
            ]
          }
        },
        "required": [
          "name",
          "required",
          "allow_multiple",
          "file"
        ]
      }
    }
  },
  "required": [
    "_id",
    "name",
    "short_description",
    "long_description",
    "title",
    "owner",
    "keywords",
    "keywords_tool",
    "infrastructure",
    "input_files",
    "input_files_public_dir",
    "arguments",
    "output_files"
  ],
  "additionalProperties": false,
  "definitions": {
    "cloud": {
      "oneOf": [
        {
          "$ref": "#/definitions/SGE"
        },
        {
          "$ref": "#/definitions/PMES"
        }
      ]
    },
    "SGE": {
      "type": "object",
      "properties": {
        "launcher": {
          "type": "string",
          "pattern": "^SGE$"
        },
        "default_cloud": {
          "type": "boolean",
          "default": false
        }
      },
      "required": [
        "launcher"
      ],
      "additionalProperties": false
    },
    "PMES": {
      "type": "object",
      "properties": {
        "launcher": {
          "type": "string",
          "pattern": "^PMES$"
        },
        "workflowType": {
          "type": "string",
          "enum": [
            "Single",
            "COMPSs"
          ],
          "default": "Single"
        },
        "default_cloud": {
          "type": "boolean",
          "default": false
        },
        "minimumVMs": {
          "type": "integer",
          "default": 1
        },
        "initialVMs": {
          "type": "integer",
          "default": 1
        }
      },
      "required": [
        "launcher"
      ],
      "additionalProperties": false
    }
  }
}