[
    {
        "id": "IBS_gds",
        "name": "identity-by-state IBS",
        "article": "",
        "website": "",
        "git": "",
        "description": "identity-by-state (IBS) estimation with SNPRelate of the fraction of identity by state for each pair of samples",
        "version": "1.32.0",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "IBS_gds",
                "command": "",
                "category": "genet_pop",
                "output_dir": "IBS_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": "ibs",
                        "type": "txt",
                        "file": "*_ibs.txt",
                        "description": "a matrix of IBS proportion"
                    },
                    {
                        "name": "ibs_dendro_png",
                        "type": "png",
                        "file": "ibs_dendro_plot_mqc.png",
                        "description": "HClust and determine groups of individuals by population information or automatically"
                    },
                    {
                        "name": "ibs_heatmap_png",
                        "type": "png",
                        "file": "ibs_heatmap_mqc.png",
                        "description": "A heatmap of IBS pairwise identities"
                    },
                    {
                        "name": "ibs_mdscale_png",
                        "type": "png",
                        "file": "ibs_mdscale_mqc.png",
                        "description": "Multidimensional scaling analysis on the matrix of genome-wide IBS pairwise distances"
                    }
                ],
                "options": [
                    {
                        "name": "IBS_gds_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "script": "IBS_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."
            ]
        },
        "yaml": "{\n  id: IBS_gds,\n  name: identity-by-state IBS,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"identity-by-state (IBS) estimation with SNPRelate of the fraction of identity by state for each pair of samples\",\n  version: \"1.32.0\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: IBS_gds,\n        command: \"\",\n        category: \"genet_pop\",\n        output_dir: IBS_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: ibs, type: \"txt\", file: \"*_ibs.txt\", description: \"a matrix of IBS proportion\" },\n          { name: ibs_dendro_png, type: \"png\", file: \"ibs_dendro_plot_mqc.png\", description: \"HClust and determine groups of individuals by population information or automatically\" },\n          { name: ibs_heatmap_png, type: \"png\", file: \"ibs_heatmap_mqc.png\", description: \"A heatmap of IBS pairwise identities\" },\n          { name: ibs_mdscale_png, type: \"png\", file: \"ibs_mdscale_mqc.png\", description: \"Multidimensional scaling analysis on the matrix of genome-wide IBS pairwise distances\" },\n\n          \n        ],\n        options: [\n         \n          {\n              name: \"IBS_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: IBS_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    },\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    },\n}\n"
    }
]