[
    {
        "id": "VSEARCH_clust_unoise_OTU",
        "name": "VSEARCH Unoise rm chimera OTU",
        "article": "10.7717\/peerj.2584",
        "website": "",
        "git": "https:\/\/github.com\/torognes\/vsearch",
        "description": "Denoising of the fasta sequences in filename according to the UNOISE3 algorithm (Robert Edgar), chimera removal and OTU output",
        "version": "2.23.0",
        "documentation": "https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf",
        "multiqc": "custom",
        "commands": [
            {
                "name": "VSEARCH_clust_unoise_OTU",
                "command": "vsearch ",
                "category": "VSEARCH",
                "output_dir": "VSEARCH_clust_unoise_OTU",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "fasta_file",
                        "description": "dereplicated fasta file"
                    },
                    {
                        "name": "ucfile",
                        "type": "tsv",
                        "description": "uc file for dereplicated"
                    },
                    {
                        "name": "allfasta",
                        "type": "fasta_file",
                        "description": "all fasta file before dereplication"
                    }
                ],
                "outputs": [
                    {
                        "name": "centroids",
                        "type": "fasta_file",
                        "file": "unoise-nonchimaras.fasta",
                        "description": "Fasta Clustered, denovo chimera removed and relabel with OTU_n"
                    },
                    {
                        "name": "otutab",
                        "type": "tsv",
                        "file": "unoise-nonchimaras-OTU.tsv",
                        "description": "OTU table abundances"
                    }
                ],
                "options": [
                    {
                        "name": "VSEARCH_clust_unoise_OTU_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "VSEARCH_clust_unoise_OTU_minsize",
                        "prefix": "--minsize",
                        "type": "numeric",
                        "min": 0,
                        "max": 100,
                        "step": 1,
                        "value": 4,
                        "label": "Keep denoised reads that are present at equal to or greater than the given number of reads"
                    },
                    {
                        "name": "VSEARCH_clust_unoise_OTU_alpha",
                        "prefix": "--unoise_alpha",
                        "type": "numeric",
                        "min": 1,
                        "max": 30,
                        "step": 1,
                        "value": 2,
                        "label": "Determines the threshold level of dissimilarity (alpha unoise) between frequent and infrequent reads for exclusion of infrequent reads"
                    }
                ]
            }
        ],
        "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_clust_unoise_OTU,\n  name: VSEARCH Unoise rm chimera OTU,\n  article: \"10.7717\/peerj.2584\",\n  website: \"\",\n  git: \"https:\/\/github.com\/torognes\/vsearch\",\n  description: \"Denoising of the fasta sequences in filename according to the UNOISE3 algorithm (Robert Edgar), chimera removal and OTU output\",\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_clust_unoise_OTU,\n        command: \"vsearch \",\n        category: \"VSEARCH\",\n        output_dir: VSEARCH_clust_unoise_OTU,\n        inputs: [\n            { name: fasta, type: \"fasta_file\", description: \"dereplicated fasta file\"},\n            { name: ucfile, type: \"tsv\", description: \"uc file for dereplicated\"},\n            { name: allfasta, type: \"fasta_file\", description: \"all fasta file before dereplication\"}\n        ],\n        outputs: [\n        { name: \"centroids\", type: \"fasta_file\", file: \"unoise-nonchimaras.fasta\", description: \"Fasta Clustered, denovo chimera removed and relabel with OTU_n\" },\n        { name: \"otutab\", type: \"tsv\", file: \"unoise-nonchimaras-OTU.tsv\", description: \"OTU table abundances\" },\n        ],\n        options: [\n          {\n              name: \"VSEARCH_clust_unoise_OTU_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_clust_unoise_OTU_minsize\",\n            prefix: \"--minsize\",\n            type: \"numeric\",\n            min: 0,\n            max: 100,\n            step: 1,\n            value: 4,\n            label: \"Keep denoised reads that are present at equal to or greater than the given number of reads\",\n          },\n          {\n            name: \"VSEARCH_clust_unoise_OTU_alpha\",\n            prefix: \"--unoise_alpha\",\n            type: \"numeric\",\n            min: 1,\n            max: 30,\n            step: 1,\n            value: 2,\n            label: \"Determines the threshold level of dissimilarity (alpha unoise) between frequent and infrequent reads for exclusion of infrequent reads\",\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"
    }
]