[
    {
        "id": "makeblastdb",
        "name": "Make Blast database",
        "article": "10.1186\/1471-2105-10-421",
        "website": "https:\/\/blast.ncbi.nlm.nih.gov",
        "git": "",
        "description": "Make Blast database",
        "version": "2.14.0",
        "documentation": "https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK279690\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "makeblastdb",
                "cname": "Make Blast db",
                "command": "makeblastdb",
                "category": "blast",
                "output_dir": "blastdb",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta file input",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "database",
                        "type": "blast_db",
                        "file": "",
                        "description": "Blast database"
                    }
                ],
                "options": [
                    {
                        "name": "makeblastdb_genome_fasta",
                        "type": "input_file",
                        "value": "\/Data\/mbb_tests\/fastas\/Mock.filtered.fasta",
                        "label": "Path to reference genome fasta file"
                    },
                    {
                        "name": "makeblastdb_dbtype",
                        "prefix": "-dbtype",
                        "type": "select",
                        "choices": [
                            {
                                "nucl": "nucl"
                            },
                            {
                                "prot": "prot"
                            }
                        ],
                        "value": "nucl",
                        "label": "Molecule type of input"
                    },
                    {
                        "name": "makeblastdb_dbname",
                        "prefix": "",
                        "type": "text",
                        "value": "blastdb",
                        "label": "Name of database (No space or specific character)"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "blast": [
                "Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). https:\/\/doi.org\/10.1186\/1471-2105-10-421"
            ]
        },
        "yaml": "{\n  id: makeblastdb,\n  name: Make Blast database,\n  article: 10.1186\/1471-2105-10-421,\n  website: \"https:\/\/blast.ncbi.nlm.nih.gov\",\n  git: \"\",\n  description: \"Make Blast database\",\n  version: \"2.14.0\",\n  documentation: \"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK279690\/\",\n  multiqc:  \"custom\",\n  commands:\n    [\n      {\n        name: \"makeblastdb\",\n        cname: \"Make Blast db\",\n        command: \"makeblastdb\",\n        category: \"blast\",\n        output_dir: \"blastdb\",\n        inputs: [\n          { name: genome_fasta, type: \"contigs\", description: \"Fasta file input\", from: \"parameter\" } # you have to add it to options !!!\n        ],\n        outputs:\n        [\n          { name: database, type: \"blast_db\", file: \"\", description: \"Blast database\" },\n        ],\n        options:\n          [\n            {\n              name: makeblastdb_genome_fasta,\n              type: input_file,\n              value: \"\/Data\/mbb_tests\/fastas\/Mock.filtered.fasta\",\n              label: \"Path to reference genome fasta file\",\n            },\n            {\n              name: \"makeblastdb_dbtype\",\n              prefix: \"-dbtype\",\n              type: \"select\",\n              choices:\n                [\n                  nucl: \"nucl\",\n                  prot: \"prot\",\n                ],\n              value: \"nucl\",\n              label: \"Molecule type of input\",\n            },\n            {\n              name: \"makeblastdb_dbname\",\n              prefix: \"\",\n              type: \"text\",\n              value: \"blastdb\",\n              label: \"Name of database (No space or specific character)\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # blast: [\n    #   \"cd \/opt\/biotools\/\",\n    #   \"wget -O ncbi-blast-2.12.0+.tar.gz https:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.12.0\/ncbi-blast-2.12.0+-x64-linux.tar.gz\",\n    #   \"tar -xvzf ncbi-blast-2.12.0+.tar.gz\",\n    #   \"ENV PATH=$PATH:\/opt\/biotools\/ncbi-blast-2.12.0+\/bin\"\n    # ],\n  },\n  citations:  {\n    blast: [\n      \"Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). https:\/\/doi.org\/10.1186\/1471-2105-10-421\"\n    ]\n  }\n}\n"
    }
]