[
    {
        "id": "VSEARCH_abundance_table",
        "name": "VSEARCH generate abundance table",
        "article": "10.7717\/peerj.2584",
        "website": "",
        "git": "https:\/\/github.com\/torognes\/vsearch",
        "description": "Search strictly identical sequences contained for each sample fasta file presents in a fasta file (OTU\/ZOTU\/ASV database)",
        "version": "2.23.0",
        "documentation": "https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf",
        "multiqc": "custom",
        "commands": [
            {
                "name": "VSEARCH_abundance_table",
                "command": "vsearch ",
                "category": "VSEARCH",
                "output_dir": "VSEARCH_abundance_table",
                "inputs": [
                    {
                        "name": "fasta_dir",
                        "type": "fasta_dir",
                        "description": "Directory containing fasta files *.fasta *.fas *.fa for each sample"
                    },
                    {
                        "name": "fasta_file",
                        "type": "fasta_file",
                        "description": "File define as database fasta files *.fasta *.fas *.fa"
                    }
                ],
                "outputs": [
                    {
                        "name": "centroids",
                        "type": "fasta_file",
                        "file": "RefSequence.fasta",
                        "description": "Nucleotidic fasta sequence of referenced OTU"
                    },
                    {
                        "name": "otutab",
                        "type": "tsv",
                        "file": "Abundance_Table.tsv",
                        "description": "OTU table abundances"
                    }
                ],
                "options": [
                    {
                        "name": "VSEARCH_abundance_table_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "VSEARCH_abundance_table_clustering_step",
                        "prefix": "",
                        "type": "radio",
                        "choices": [
                            {
                                "1": "True"
                            },
                            {
                                "": "False"
                            }
                        ],
                        "value": "False",
                        "label": "Do you want to append a clustering step on OTU\/ZOTU\/ASV (the fasta file used as database)?"
                    },
                    {
                        "name": "VSEARCH_abundance_table_clustering_identity",
                        "prefix": "--id",
                        "type": "numeric",
                        "min": "0",
                        "max": "1",
                        "step": "0.01",
                        "value": "0.97",
                        "label": "Set this parameter is used only if clustering step is set. Pairwize identity ((matching columns) \/ (alignment length - terminal gaps))"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "VSEARCH": [
                "Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584."
            ]
        },
        "yaml": "{\n  id: VSEARCH_abundance_table,\n  name: VSEARCH generate abundance table,\n  article: \"10.7717\/peerj.2584\",\n  website: \"\",\n  git: \"https:\/\/github.com\/torognes\/vsearch\",\n  description: \"Search strictly identical sequences contained for each sample fasta file presents in a fasta file (OTU\/ZOTU\/ASV database)\",\n  version: \"2.23.0\",\n  documentation: \"https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: VSEARCH_abundance_table,\n        command: \"vsearch \",\n        category: \"VSEARCH\",\n        output_dir: VSEARCH_abundance_table,\n        inputs: [\n          { name: fasta_dir, type: \"fasta_dir\", description: \"Directory containing fasta files *.fasta *.fas *.fa for each sample\"},\n          { name: fasta_file, type: \"fasta_file\", description: \"File define as database fasta files *.fasta *.fas *.fa\"}\n        ],\n        outputs: [\n          { name: \"centroids\", type: \"fasta_file\", file: \"RefSequence.fasta\", description: \"Nucleotidic fasta sequence of referenced OTU\" },\n          { name: \"otutab\", type: \"tsv\", file: \"Abundance_Table.tsv\", description: \"OTU table abundances\" },\n        ],\n        options: [\n          {\n            name: \"VSEARCH_abundance_table_threads\",\n            prefix: \"--threads\",\n            value: 16,\n            min: 1,\n            max: 64,\n            step: 1,\n            label: \"Threads to use\",\n            type: \"numeric\",\n          },\n          {\n            name: \"VSEARCH_abundance_table_clustering_step\",\n            prefix: \"\",\n            type:  \"radio\",\n            choices:\n              [\n                True: \"True\",\n                False: \"False\",\n              ],\n              value: \"False\",\n              label: \"Do you want to append a clustering step on OTU\/ZOTU\/ASV (the fasta file used as database)?\",\n          },\n          {\n            name: \"VSEARCH_abundance_table_clustering_identity\",\n            prefix: \"--id\",\n            type: \"numeric\",\n            min: \"0\",\n            max: \"1\",\n            step: \"0.01\",\n            value: \"0.97\",\n            label: \"Set this parameter is used only if clustering step is set. Pairwize identity ((matching columns) \/ (alignment length - terminal gaps))\",\n          },\n        ],\n      },\n    ],\n  install:\n    {\n      # VSEARCH: [\n      #   \"cd \/opt\/biotools\/\",\n      #   \" wget https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch-2.21.1-linux-x86_64.tar.gz\",\n      #   \" tar -zxvf vsearch-2.21.1-linux-x86_64.tar.gz\",\n      #   \" mv vsearch-2.21.1-linux-x86_64\/bin\/vsearch \/opt\/biotools\/bin\",\n      #   \" rm -rf vsearch-2.21.1-linux-x86_64*\"\n      # ]\n    },\n  citations:\n    {\n      VSEARCH: [\n        \"Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584.\"\n      ]\n    },\n}\n"
    }
]