[
    {
        "id": "lulu",
        "name": "lulu post clustering",
        "article": "https:\/\/www.nature.com\/articles\/s41467-017-01312-x",
        "website": "https:\/\/github.com\/tobiasgf\/lulu",
        "git": "https:\/\/github.com\/tobiasgf\/lulu",
        "description": "A r-package for distribution based post clustering curation of amplicon data.",
        "version": "1.0.0",
        "documentation": "https:\/\/github.com\/tobiasgf\/lulu",
        "multiqc": "custom",
        "commands": [
            {
                "name": "lulu",
                "cname": "lulu post clustering",
                "command": "",
                "category": "metabarcoding",
                "output_dir": "lulu",
                "inputs": [
                    {
                        "name": "abundance_file",
                        "type": "tsv",
                        "file": "abundance.tsv",
                        "description": "OTU table with samples as columns and OTUs as rows, with unique OTU id's as row names"
                    },
                    {
                        "name": "sequence_file",
                        "type": "fasta_file",
                        "file": "OTU_seqs.fasta",
                        "description": "OTU sequences"
                    }
                ],
                "outputs": [
                    {
                        "name": "curated_table",
                        "type": "tsv",
                        "file": "curated_table.tsv",
                        "description": "Table of retained OTUs"
                    },
                    {
                        "name": "otu_map",
                        "type": "tsv",
                        "file": "otu_map.tsv",
                        "description": "Table of information of which daughters were mapped to which parents OTUs"
                    }
                ],
                "options": [
                    {
                        "name": "lulu_matcher_method",
                        "type": "radio",
                        "value": "blast",
                        "choices": [
                            {
                                "blast": "blast"
                            },
                            {
                                "vsearch": "vsearch"
                            }
                        ],
                        "label": "tool for pair wise matching of OTU sequences"
                    },
                    {
                        "name": "lulu_minimum_ratio",
                        "type": "numeric",
                        "value": 1,
                        "min": 0,
                        "max": 1,
                        "step": 0.01,
                        "label": "minimim abundance ratio between a potential error and a potential parent"
                    },
                    {
                        "name": "lulu_minimum_match",
                        "type": "numeric",
                        "value": 84,
                        "min": 0,
                        "max": 100,
                        "step": 1,
                        "label": "minimum threshold (%)of sequence similarity for considering any OTU as an error of another"
                    }
                ]
            }
        ],
        "install": {
            "lulu": [
                "Rscript -e 'devtools::install_github(\"tobiasgf\/lulu\")' "
            ]
        },
        "citations": {
            "lulu": [
                "Fr\u00f8slev, T. G., Kj\u00f8ller, R., Bruun, H. H., Ejrn\u00e6s, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188."
            ]
        },
        "yaml": "{\n  id: lulu ,\n  name: lulu post clustering,\n  article: \"https:\/\/www.nature.com\/articles\/s41467-017-01312-x\",\n  website: \"https:\/\/github.com\/tobiasgf\/lulu\",\n  git: \"https:\/\/github.com\/tobiasgf\/lulu\",\n  description: \"A r-package for distribution based post clustering curation of amplicon data.\",\n  version: \"1.0.0\",\n  documentation: \"https:\/\/github.com\/tobiasgf\/lulu\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: lulu,\n        cname: \"lulu post clustering\",\n        command: \"\",\n        category: \"metabarcoding\",\n        output_dir: lulu,\n        inputs: [\n          { name: \"abundance_file\", type: \"tsv\", file: \"abundance.tsv\", description: \"OTU table with samples as columns and OTUs as rows, with unique OTU id's as row names\" },\n          { name: sequence_file, type: \"fasta_file\", file: \"OTU_seqs.fasta\", description: \"OTU sequences\"},\n        ],\n        outputs:\n          [  \n            { name: curated_table, type: \"tsv\", file: \"curated_table.tsv\", description: \"Table of retained OTUs\" },\n            { name: otu_map, type: \"tsv\", file: \"otu_map.tsv\", description: \"Table of information of which daughters were mapped to which parents OTUs\" },\n          ],\n        options:\n          [\n            {\n              name: lulu_matcher_method,\n              type: radio,\n              value: \"blast\",\n              choices: [blast: blast, vsearch: vsearch],\n              label: \"tool for pair wise matching of OTU sequences\",\n            },\n            {\n              name: lulu_minimum_ratio,\n              type: numeric,\n              value: 1,\n              min: 0,\n              max: 1,\n              step: 0.01,\n              label: \"minimim abundance ratio between a potential\n          error and a potential parent\",\n            },\n            {\n              name: lulu_minimum_match,\n              type: numeric,\n              value: 84,\n              min: 0,\n              max: 100,\n              step: 1,\n              label: \"minimum threshold (%)of sequence similarity for considering\n          any OTU as an error of another\",\n            }\n          ],\n      },\n    ],\n  install: {\n      lulu: [\n        \"Rscript -e 'devtools::install_github(\\\"tobiasgf\/lulu\\\")' \"\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      # 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  },\n  citations:  {\n    lulu: [\n      \"Fr\u00f8slev, T. G., Kj\u00f8ller, R., Bruun, H. H., Ejrn\u00e6s, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188.\"\n    ],\n  }\n}"
    }
]