[
    {
        "id": "FstPiDxy_Manhattan",
        "name": "FstPiDxy_Manhattan",
        "article": "",
        "website": "https:\/\/mbb.univ-montp2.fr",
        "git": "https:\/\/github.com\/jashapiro\/fastStructure",
        "description": "Manhattan plot of Fs, Pi and Dxy pairwise values on sliding windows",
        "version": "1.38.0",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "FstPiDxy_Manhattan",
                "command": "",
                "category": "genet_pop",
                "output_dir": "FstPiDxy_Manhattan",
                "inputs": [
                    {
                        "name": "gds",
                        "type": "gds",
                        "file": "",
                        "description": "Multisample gds file"
                    },
                    {
                        "name": "popmap_file",
                        "type": "popmap",
                        "file": "",
                        "description": "Path to tsv file with samples group"
                    }
                ],
                "outputs": [
                    {
                        "name": "manhattan_done",
                        "type": "txt",
                        "file": "manhattan_done.txt",
                        "description": "dir containing plots and Fst outliers"
                    }
                ],
                "options": [
                    {
                        "name": "FstPiDxy_Manhattan_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "FstPiDxy_Manhattan_windSize",
                        "prefix": "-w",
                        "value": 500,
                        "min": 100,
                        "max": 100000,
                        "step": 10,
                        "label": "Sliding windows size(bp)",
                        "type": "numeric"
                    },
                    {
                        "name": "FstPiDxy_Manhattan_quantil",
                        "prefix": "-q",
                        "value": 99,
                        "min": 10,
                        "max": 100,
                        "step": 1,
                        "label": "color in red windows w\/ mean(Fst) > quantile(%)",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "script": "FstPiDxy_Manhattan.R",
        "install": [],
        "citations": {
            "SeqArray": [
                "Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir B, Laurie C, Levine D (2017). SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi: 10.1093\/bioinformatics\/btx145."
            ]
        },
        "yaml": "{\n  id: FstPiDxy_Manhattan,\n  name: FstPiDxy_Manhattan,\n  article: \"\",\n  website: \"https:\/\/mbb.univ-montp2.fr\",\n  git: \"https:\/\/github.com\/jashapiro\/fastStructure\",\n  description: \"Manhattan plot of Fs, Pi and Dxy pairwise values on sliding windows\",\n  version: \"1.38.0\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [ \n      {\n        name: FstPiDxy_Manhattan,\n        command: \"\",\n        category: \"genet_pop\",\n        output_dir: FstPiDxy_Manhattan,\n        inputs: [\n                 { name: gds, type: \"gds\", file: \"\",description: \"Multisample gds file\"} ,\n                 { name: popmap_file, type: \"popmap\", file: \"\", description: \"Path to tsv file with samples group\"}\n                ],\n        outputs: [\n          { name: \"manhattan_done\", type: \"txt\", file: \"manhattan_done.txt\", description: \"dir containing plots and Fst outliers\" },\n          #name: manhattan, type: \"png\", file: \"manhattan_mqc.png\", description: \"Manhattan plot of Fs, Pi and Dxy pairwise values on sliding windows\" },\n        ],\n        options: [\n          {\n              name: \"FstPiDxy_Manhattan_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: \"FstPiDxy_Manhattan_windSize\",\n              prefix: \"-w\",\n              value: 500,\n              min: 100,\n              max: 100000,\n              step: 10,\n              label: \"Sliding windows size(bp)\",\n              type: \"numeric\",\n          },\n          {\n              name: \"FstPiDxy_Manhattan_quantil\",\n              prefix: \"-q\",\n              value: 99,\n              min: 10,\n              max: 100,\n              step: 1,\n              label: \"color in red windows w\/ mean(Fst) > quantile(%)\",\n              type: \"numeric\",\n          },\n        ],\n      },\n    ],\n  script:  FstPiDxy_Manhattan.R,\n  install:\n    {\n      # SeqArray: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SeqArray\", update = TRUE, ask = FALSE)'' '\n      # ],\n    },\n  citations:\n    {\n     SeqArray: [\n       \"Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir B, Laurie C, Levine D (2017). SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi: 10.1093\/bioinformatics\/btx145.\" \n       ],\n    },\n}\n"
    }
]