[
    {
        "id": "gblocks",
        "name": "Gblocks",
        "article": "10.1093\/oxfordjournals.molbev.a026334",
        "website": "http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html",
        "git": "",
        "description": "Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.",
        "version": "0.91b",
        "documentation": "http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html",
        "multiqc": "custom",
        "commands": [
            {
                "name": "gblocks",
                "cname": "Gblocks",
                "command": "Gblocks",
                "category": "phylogenetics",
                "output_dir": "gblocks",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "aligned_fasta",
                        "file": "*.fasta",
                        "description": "Aligned fasta file",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "clean_fasta",
                        "type": "aligned_fasta",
                        "file": "*.fasta",
                        "description": "Cleaned aligned fasta file"
                    },
                    {
                        "name": "report",
                        "type": "html",
                        "file": "out.fasta-gb_mqc.html",
                        "description": "Report file"
                    }
                ],
                "options": [
                    {
                        "name": "gblocks_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to fasta file"
                    },
                    {
                        "name": "gblocks_seqtype",
                        "type": "radio",
                        "choices": [
                            {
                                "Protein": "p"
                            },
                            {
                                "DNA": "d"
                            },
                            {
                                "Codons": "c"
                            }
                        ],
                        "value": "d",
                        "label": "Type Of Sequence"
                    },
                    {
                        "name": "gblocks_b1",
                        "prefix": "-b1=",
                        "type": "numeric",
                        "value": "NA",
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum Number Of Sequences For A Conserved Position (50% of the number of sequences + 1). Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences"
                    },
                    {
                        "name": "gblocks_b2",
                        "prefix": "-b2=",
                        "type": "numeric",
                        "value": "NA",
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum Number Of Sequences For A Flank Position (85% of the number of sequences). Any integer equal or bigger than Minimum Number Of Sequences For A Conserved Position"
                    },
                    {
                        "name": "gblocks_b3",
                        "prefix": "-b3=",
                        "type": "numeric",
                        "value": 8,
                        "min": "NA",
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum Number Of Contiguous Nonconserved Positions"
                    },
                    {
                        "name": "gblocks_b4",
                        "prefix": "-b4=",
                        "type": "numeric",
                        "value": 10,
                        "min": 2,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum Length Of A Block"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "gblocks": [
                "J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, Volume 17, Issue 4, April 2000, Pages 540-552, https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a026334"
            ]
        },
        "yaml": "{\n  id: gblocks,\n  name: Gblocks ,\n  article: \"10.1093\/oxfordjournals.molbev.a026334\",\n  website: \"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html\",\n  git: \"\",\n  description: \"Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.\",\n  version: \"0.91b\",\n  documentation: \"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: gblocks,\n        cname: \"Gblocks\",\n        command: \"Gblocks\",\n        category: \"phylogenetics\",\n        output_dir: gblocks,\n        inputs: [{ name: fasta, type: \"aligned_fasta\", file: \"*.fasta\", description: \"Aligned fasta file\", from: \"parameter\"}],\n        outputs: [{ name: clean_fasta, type: \"aligned_fasta\", file: \"*.fasta\", description: \"Cleaned aligned fasta file\"},\n        { name: report, type: \"html\", file: \"out.fasta-gb_mqc.html\", description: \"Report file\"}\n        ],\n        options: [\n          {\n            name: gblocks_fasta,\n            type: input_file,\n            value: \"\",\n            label: \"Path to fasta file\",\n          },\n          {\n              name: gblocks_seqtype,\n              type: radio,\n              choices:\n                [\n                  Protein: \"p\",\n                  DNA: \"d\",\n                  Codons: \"c\"\n                ],\n              value: \"d\",\n              label: \"Type Of Sequence\",\n            },\n            {\n              name: \"gblocks_b1\",\n              prefix: \"-b1=\",\n              type: \"numeric\",\n              value: NA,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Minimum Number Of Sequences For A Conserved Position (50% of the number of sequences + 1). Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences\",\n            },\n            {\n              name: \"gblocks_b2\",\n              prefix: \"-b2=\",\n              type: \"numeric\",\n              value: NA ,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Minimum Number Of Sequences For A Flank Position (85% of the number of sequences). Any integer equal or bigger than Minimum Number Of Sequences For A Conserved Position\",\n            },\n            {\n              name: \"gblocks_b3\",\n              prefix: \"-b3=\",\n              type: \"numeric\",\n              value: 8 ,\n              min: NA,\n              max: NA,\n              step: 1,\n              label: \"Maximum Number Of Contiguous Nonconserved Positions\",\n            },\n            {\n              name: \"gblocks_b4\",\n              prefix: \"-b4=\",\n              type: \"numeric\",\n              value: 10,\n              min: 2,\n              max: NA,\n              step: 1,\n              label: \"Minimum Length Of A Block\",\n            },\n        ],\n      },\n    ],\n  install:\n    {\n      # gblocks: [\n      #   \"cd \/opt\/biotools\/\",\n      #   \"wget http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_Linux64_0.91b.tar.Z\",\n      #   \"tar -xvzf Gblocks_Linux64_0.91b.tar.Z\",\n      #   \"mv Gblocks_0.91b\/Gblocks bin\/\",\n      #   \"rm -r Gblocks_Linux64_0.91b.tar.Z Gblocks_0.91b\"\n      # ]\n    },\n  citations:\n    {\n      gblocks: [\n        \"J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, Volume 17, Issue 4, April 2000, Pages 540-552, https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a026334\"\n      ]\n    },\n}\n"
    }
]