[
    {
        "id": "sfs_outgroup",
        "name": "sfs outgroup",
        "article": "10.1186\/1471-2105-10-421",
        "website": "https:\/\/blast.ncbi.nlm.nih.gov",
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/ibonnici\/snom",
        "description": "BLAST programs search nucleotide databases using a nucleotide query",
        "version": "2.14.0",
        "documentation": "https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK279690\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "sfs_outgroup",
                "cname": "sfs_outgroup",
                "command": "blastn",
                "category": "blast",
                "output_dir": "sfs_outgroup",
                "inputs": [
                    {
                        "name": "query",
                        "type": "fasta_file",
                        "description": "Fasta query file",
                        "from": "parameter"
                    },
                    {
                        "name": "blastdb_dir",
                        "type": "blast_db",
                        "file": "",
                        "description": "Blast database",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "blastout",
                        "type": "tsv",
                        "file": "blastout*.tsv",
                        "description": "Blast output"
                    },
                    {
                        "name": "sfs_outgroup",
                        "type": "sfs",
                        "file": "outgroup.sfs.count",
                        "description": "specific nucleotide count as est-sfs outgroup format"
                    }
                ],
                "options": [
                    {
                        "name": "sfs_outgroup_query",
                        "type": "input_file",
                        "value": "\/Data\/mbb_tests\/low\/reference\/genome\/query.fa",
                        "label": "Path to query fasta file"
                    },
                    {
                        "name": "sfs_outgroup_blastdb_dir",
                        "type": "input_dir",
                        "value": "\/Data\/mbb_tests\/low\/reference\/genome\/blast_db\/",
                        "label": "Path to a blast database directory"
                    },
                    {
                        "name": "sfs_outgroup_threads",
                        "prefix": "-cpu",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "blast_max_target_sequences",
                        "prefix": "-max_target_seqs",
                        "type": "numeric",
                        "value": 10,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of aligned sequences to keep"
                    },
                    {
                        "name": "blast_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"
                    }
                ]
            }
        ],
        "install": [],
        "assets": [
            "snom"
        ],
        "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"
            ],
            "snom": [
                "Bonnici I. https:\/\/gitlab.mbb.univ-montp2.fr\/ibonnici\/snom"
            ]
        },
        "yaml": "{\n  id: sfs_outgroup,\n  name: sfs outgroup,\n  article: 10.1186\/1471-2105-10-421,\n  website: \"https:\/\/blast.ncbi.nlm.nih.gov\",\n  git: \"https:\/\/gitlab.mbb.univ-montp2.fr\/ibonnici\/snom\",\n  description: \"BLAST 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:  \"custom\", # from mbb_mqc_plugin\n  commands:\n    [\n      {\n        name: \"sfs_outgroup\",\n        cname: \"sfs_outgroup\",\n        command: \"blastn\",\n        category: \"blast\",\n        output_dir: \"sfs_outgroup\",\n        inputs: \n        [\n          { name: query, type: \"fasta_file\", description: \"Fasta query file\",  from: \"parameter\" }, \n          { name: blastdb_dir, type: \"blast_db\", file: \"\", description: \"Blast database\",  from: \"parameter\" }\n        ],\n        outputs:\n        [\n          { name: blastout, type: \"tsv\", file: \"blastout*.tsv\", description: \"Blast output\" },\n          { name: sfs_outgroup, type: \"sfs\", file: \"outgroup.sfs.count\", description: \"specific nucleotide count as est-sfs outgroup format\" }\n        ],\n        options:\n          [\n            {\n              name: sfs_outgroup_query,\n              type: input_file,\n              value: \"\/Data\/mbb_tests\/low\/reference\/genome\/query.fa\",\n              label: \"Path to query fasta file\",\n            },\n            {\n              name: sfs_outgroup_blastdb_dir,\n              type: input_dir,\n              value: \"\/Data\/mbb_tests\/low\/reference\/genome\/blast_db\/\",\n              label: \"Path to a blast database directory\",\n            },\n            {\n              name: sfs_outgroup_threads,\n              prefix: -cpu,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: \"blast_max_target_sequences\",\n              prefix: \"-max_target_seqs\",\n              type: numeric,\n              value: 10,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of aligned sequences to keep\",\n            },\n            {\n              name: \"blast_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: \"blast_out\",\n            #   type: \"checkboxGroupInput\",\n            #   choices: [\n            #     qseqid: \"qseqid\",\n            #     sseqid: \"sseqid\",\n            #     pident: \"pident\",\n            #     qcov: \"qcov\",\n            #     length: \"length\",\n            #     mismatch: \"mismatch\",\n            #     gapopen: \"gapopen\",\n            #     qstart: \"qstart\",\n            #     qend: \"qend\",\n            #     qseq: \"qseq\",\n            #     sstart: \"sstart\",\n            #     send: \"send\",\n            #     sseq: \"sseq\",\n            #     evalue: \"evalue\",\n            #     bitscore: \"bitscore\",\n            #     qlen: \"qlen\",\n            #     slen: \"slen\",\n            #     btop: \"btop\"\n            #   ],\n            #   value: [\n            #     qseqid,\n            #     pident,\n            #     qstart,\n            #     qend,\n            #     qseq,\n            #     sstart,\n            #     send,\n            #     sseq,\n            #     btop\n            #   ],\n            #   label: \"Blast out format\"\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  assets:  [\"snom\"],\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    snom: [\n      \"Bonnici I. https:\/\/gitlab.mbb.univ-montp2.fr\/ibonnici\/snom\"\n    ]\n  }\n}\n"
    }
]