[
    {
        "id": "blastn_ncbi",
        "name": "BlastN NCBI",
        "article": "10.1186\/1471-2105-10-421",
        "website": "https:\/\/blast.ncbi.nlm.nih.gov",
        "git": "",
        "description": "BLASTN programs search nucleotide databases using a nucleotide query",
        "version": "2.14.0",
        "documentation": "https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK279690\/",
        "multiqc": "blast",
        "commands": [
            {
                "name": "blastn_ncbi",
                "cname": "BlastN NCBI",
                "command": "blastn",
                "category": "blast",
                "output_dir": "blastn_ncbi",
                "inputs": [
                    {
                        "name": "query",
                        "type": "fasta",
                        "description": "Fasta query file",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "blastout",
                        "type": "tsv",
                        "file": "blastout*.tsv",
                        "description": "Blast output"
                    }
                ],
                "options": [
                    {
                        "name": "blastn_ncbi_query",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to query fasta file"
                    },
                    {
                        "name": "blastn_ncbi_remote_db",
                        "prefix": "",
                        "type": "select",
                        "choices": [
                            {
                                "nt": "nt"
                            }
                        ],
                        "value": "nt",
                        "label": "Remote NCBI blast database"
                    },
                    {
                        "name": "blastn_ncbi_evalue",
                        "prefix": "-evalue",
                        "type": "numeric",
                        "value": 0.1,
                        "min": 0,
                        "max": "NA",
                        "step": 0.01,
                        "label": "e-value"
                    },
                    {
                        "name": "blastn_ncbi_max_target_sequences",
                        "prefix": "-max_target_seqs",
                        "type": "numeric",
                        "value": 1,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of aligned sequences to keep"
                    },
                    {
                        "name": "blastn_ncbi_max_hsps",
                        "prefix": "-max_hsps",
                        "type": "numeric",
                        "value": 3,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum number of HSPs (alignments) to keep for any single query-subject pair"
                    },
                    {
                        "name": "blastn_ncbi_min_len",
                        "prefix": "",
                        "type": "numeric",
                        "value": 50,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Blast min align length"
                    }
                ]
            }
        ],
        "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: blastn_ncbi,\n  name: BlastN NCBI,\n  article: 10.1186\/1471-2105-10-421,\n  website: \"https:\/\/blast.ncbi.nlm.nih.gov\",\n  git: \"\",\n  description: \"BLASTN programs search nucleotide databases using a nucleotide query\",\n  version: \"2.14.0\",\n  documentation: \"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK279690\/\",\n  multiqc:  \"blast\", # from mbb_mqc_plugin\n  commands:\n    [\n      {\n        name: \"blastn_ncbi\",\n        cname: \"BlastN NCBI\",\n        command: \"blastn\",\n        category: \"blast\",\n        output_dir: \"blastn_ncbi\",\n        inputs: [\n          { name: query, type: \"fasta\", description: \"Fasta query file\" , from: \"parameter\" },\n        ],\n        outputs:\n        [\n          { name: blastout, type: \"tsv\", file: \"blastout*.tsv\", description: \"Blast output\" },\n        ],\n        options:\n          [\n            {\n              name: blastn_ncbi_query,\n              type: input_file,\n              value: \"\",\n              label: \"Path to query fasta file\",\n            },\n            {\n              name: \"blastn_ncbi_remote_db\",\n              prefix: \"\",\n              type: \"select\",\n              choices:\n                [\n                  nt: \"nt\",\n                ],\n              value: \"nt\",\n              label: \"Remote NCBI blast database\",\n            },\n            {\n              name: blastn_ncbi_evalue,\n              prefix: \"-evalue\",\n              type: numeric,\n              value: 0.1,\n              min: 0,\n              max: NA,\n              step: 0.01,\n              label: \"e-value\",\n            },\n            {\n              name: \"blastn_ncbi_max_target_sequences\",\n              prefix: \"-max_target_seqs\",\n              type: numeric,\n              value: 1,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of aligned sequences to keep\",\n            },\n            {\n              name: \"blastn_ncbi_max_hsps\",\n              prefix: \"-max_hsps\",\n              type: numeric,\n              value: 3,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Maximum number of HSPs (alignments) to keep for any single query-subject pair\",\n            },\n            {\n              name: \"blastn_ncbi_min_len\",\n              prefix: \"\",\n              type: numeric,\n              value: 50,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Blast min align length\",\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    # mbb_mqc_plugin:\n    # [\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/mmassaviol\/mbb_mqc_plugin.git\",\n    #   \"cd mbb_mqc_plugin\",\n    #   \"python3 setup.py install\"\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"
    }
]