[
    {
        "id": "Fst_gds",
        "name": "W&C Fst",
        "article": "",
        "website": "",
        "git": "",
        "description": "W&C Fixation index (Fst) with SNPRelate R package",
        "version": "1.32.0",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "Fst_gds",
                "command": "",
                "category": "genet_pop",
                "output_dir": "Fst_gds",
                "inputs": [
                    {
                        "name": "gds",
                        "type": "gds",
                        "file": "",
                        "description": "gds file"
                    },
                    {
                        "name": "popmap_file",
                        "type": "popmap",
                        "file": "",
                        "description": "Path to tsv file with samples group"
                    }
                ],
                "outputs": [
                    {
                        "name": "fst",
                        "type": "txt",
                        "file": "*_fst.txt",
                        "description": "Weir and Cockerham weighted Fst estimate for each pop pair"
                    },
                    {
                        "name": "meanfst",
                        "type": "txt",
                        "file": "*_meanfst.txt",
                        "description": "Weir and Cockerham mean Fst estimate for each pop pair"
                    },
                    {
                        "name": "NJ_png",
                        "type": "png",
                        "file": "Fst_NJ_plot_mqc.png",
                        "description": "NJ tree on pop pairwise Fst"
                    },
                    {
                        "name": "Fst_heatmap_png",
                        "type": "png",
                        "file": "Fst_heatmap_mqc.png",
                        "description": "NJ tree on pop pairwise Fst"
                    }
                ],
                "options": [
                    {
                        "name": "Fst_gds_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "script": "Fst_gds.script.R",
        "install": [],
        "citations": {
            "SNPRelate": [
                "Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics, 28(24), 3326-3328. doi: 10.1093\/bioinformatics\/bts606. "
            ],
            "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."
            ],
            "ape": [
                "Paradis E, Schliep K (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526-528."
            ],
            "ggtree": [
                "Yu G (2020). Using ggtree to Visualize Data on Tree-Like Structures. Current Protocols in Bioinformatics, 69(1), e96. doi: 10.1002\/cpbi.96, https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/abs\/10.1002\/cpbi.96."
            ]
        },
        "yaml": "{\n  id: Fst_gds,\n  name: W&C Fst,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"W&C Fixation index (Fst) with SNPRelate R package\",\n  version: \"1.32.0\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: Fst_gds,\n        command: \"\",\n        category: \"genet_pop\",\n        output_dir: Fst_gds,\n        inputs: [{ name: gds, type: \"gds\", file: \"\",description: \"gds file\"} ,\n                 { name: popmap_file, type: \"popmap\", file: \"\", description: \"Path to tsv file with samples group\"}\n                ],\n        outputs: [\n          { name: fst, type: \"txt\", file: \"*_fst.txt\", description: \"Weir and Cockerham weighted Fst estimate for each pop pair\" },\n          { name: meanfst, type: \"txt\", file: \"*_meanfst.txt\", description: \"Weir and Cockerham mean Fst estimate for each pop pair\" },\n          { name: NJ_png, type: \"png\", file: \"Fst_NJ_plot_mqc.png\", description: \"NJ tree on pop pairwise Fst\" },\n          { name: Fst_heatmap_png, type: \"png\", file: \"Fst_heatmap_mqc.png\", description: \"NJ tree on pop pairwise Fst\" },\n\n          \n        ],\n        options: [\n          {\n              name: \"Fst_gds_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  script: Fst_gds.script.R,\n  install:\n    {\n      # SNPRelate: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SNPRelate\", update = TRUE, ask = FALSE)'' '\n      # ],\n      # SeqArray: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SeqArray\", update = TRUE, ask = FALSE)'' '\n      # ], \n      # ape: [\n      #   'Rscript -e ''install.packages(\"ape\")'' '\n      # ],\n      # ggtree: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"ggtree\", update = TRUE, ask = FALSE)'' '\n      # ]\n    },\n  citations:\n    {\n     SNPRelate: [\n       \"Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics, 28(24), 3326-3328. doi: 10.1093\/bioinformatics\/bts606. \" \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     ape: [\"Paradis E, Schliep K (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526-528.\"],\n     ggtree: [\"Yu G (2020). Using ggtree to Visualize Data on Tree-Like Structures. Current Protocols in Bioinformatics, 69(1), e96. doi: 10.1002\/cpbi.96, https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/abs\/10.1002\/cpbi.96.\" ]\n    },\n}\n"
    }
]