[
    {
        "id": "VSEARCH_derep_fastafile",
        "name": "VSEARCH Dereplicate file",
        "article": "10.7717\/peerj.2584",
        "website": "",
        "git": "https:\/\/github.com\/torognes\/vsearch",
        "description": "Merge strictly identical sequences contained in fasta file",
        "version": "2.23.0",
        "documentation": "https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf",
        "multiqc": "custom",
        "commands": [
            {
                "name": "VSEARCH_derep_fastafile",
                "command": "vsearch ",
                "category": "VSEARCH",
                "output_dir": "VSEARCH_derep_fastafile",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "fasta_file",
                        "description": "fasta file "
                    }
                ],
                "outputs": [
                    {
                        "name": "derepfasta",
                        "type": "fasta_file",
                        "file": "derep.fasta",
                        "description": "dereplicated sequences in fasta format sorted by decreasing abundance."
                    },
                    {
                        "name": "uclust_like",
                        "type": "tsv",
                        "file": "derep.uc",
                        "description": "tab-separated uclust-like format with 10 columns and 3 different type of entries (S, H or C)"
                    },
                    {
                        "name": "otutab",
                        "type": "tsv",
                        "file": "Derep_Table.tsv",
                        "description": "Abundance table with dereplicates sequences as row"
                    }
                ],
                "options": [
                    {
                        "name": "VSEARCH_derep_fastafile_maxuniquesize",
                        "prefix": "--maxuniquesize",
                        "type": "numeric",
                        "value": 1000,
                        "min": 1,
                        "max": 1000000,
                        "step": 1,
                        "label": "maximum abundance for output from dereplication"
                    },
                    {
                        "name": "VSEARCH_derep_fastafile_minuniquesize",
                        "prefix": "--minuniquesize",
                        "type": "numeric",
                        "value": 1,
                        "min": 1,
                        "max": 10000,
                        "step": 1,
                        "label": "minimum abundance for output from dereplication"
                    },
                    {
                        "name": "VSEARCH_derep_fastafile_sizein",
                        "prefix": "--sizein",
                        "type": "checkbox",
                        "value": true,
                        "label": "read abundance annotation from input"
                    },
                    {
                        "name": "VSEARCH_derep_fastafile_strand",
                        "type": "radio",
                        "value": "--strand plus",
                        "choices": [
                            {
                                "plus": "--strand plus"
                            },
                            {
                                "both": "--strand both"
                            }
                        ],
                        "label": "dereplicate plus or both strands"
                    },
                    {
                        "name": "VSEARCH_derep_remove_single",
                        "prefix": "--sizein",
                        "type": "checkbox",
                        "value": true,
                        "label": "remove singleton from output"
                    },
                    {
                        "name": "VSEARCH_derep_fastafile_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "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_derep_fastafile,\n  name: VSEARCH Dereplicate file,\n  article: \"10.7717\/peerj.2584\",\n  website: \"\",\n  git: \"https:\/\/github.com\/torognes\/vsearch\",\n  description: \"Merge strictly identical sequences contained in fasta file\",\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_derep_fastafile,\n        command: \"vsearch \",\n        category: \"VSEARCH\",\n        output_dir: VSEARCH_derep_fastafile,\n        inputs: [{ name: fasta, type: \"fasta_file\", description: \"fasta file \"}],\n        outputs: [\n        { name: \"derepfasta\", type: \"fasta_file\", file: \"derep.fasta\", description: \"dereplicated sequences in fasta format sorted by decreasing abundance.\" },\n        { name: \"uclust_like\", type: \"tsv\", file: \"derep.uc\", description: \"tab-separated uclust-like format with 10 columns and 3 different type of entries (S, H or C)\" },\n        { name: \"otutab\", type: \"tsv\", file: \"Derep_Table.tsv\", description: \"Abundance table with dereplicates sequences as row\" },\n        ],\n        options: [\n          {\n              name: VSEARCH_derep_fastafile_maxuniquesize,\n              prefix: --maxuniquesize,\n              type: numeric,\n              value: 1000,\n              min: 1,\n              max: 1000000,\n              step: 1,\n              label: \"maximum abundance for output from dereplication\",\n          },\n          {\n              name: VSEARCH_derep_fastafile_minuniquesize,\n              prefix: --minuniquesize,\n              type: numeric,\n              value: 1,\n              min: 1,\n              max: 10000,\n              step: 1,\n              label: \"minimum abundance for output from dereplication\",\n          },\n          {\n              name: VSEARCH_derep_fastafile_sizein,\n              prefix: '--sizein',\n              type: checkbox,\n              value: TRUE,\n              label: \"read abundance annotation from input\",\n          },\n          {\n              name: VSEARCH_derep_fastafile_strand,\n              type: radio,\n              value: \"--strand plus\",\n              choices: [plus: --strand plus, both: --strand both],\n              label: \"dereplicate plus or both strands\",\n          },\n          {\n              name: VSEARCH_derep_remove_single,\n              prefix: '--sizein',\n              type: checkbox,\n              value: TRUE,\n              label: \"remove singleton from output\",\n          },\n          {\n              name: \"VSEARCH_derep_fastafile_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      },\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"
    }
]