[
    {
        "id": "ggtree_draw_tree",
        "name": "ggtree draw tree",
        "article": "abs\/10.1002\/cpbi.96",
        "website": "https:\/\/yulab-smu.top\/treedata-book\/",
        "git": "https:\/\/github.com\/YuLab-SMU\/ggtree",
        "description": "R package for visualization of phylogenetic trees with their annotation data",
        "version": "3.6.0",
        "documentation": "https:\/\/yulab-smu.top\/treedata-book\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "ggtree_draw_tree",
                "cname": "ggtree draw tree",
                "command": "Rscript",
                "category": "phylogenetics",
                "output_dir": "ggtree_draw_tree",
                "inputs": [
                    {
                        "name": "tree_file",
                        "type": "newick",
                        "file": "",
                        "description": "Newick tree file",
                        "from": "parameter"
                    },
                    {
                        "name": "popmap",
                        "type": "popmap"
                    }
                ],
                "outputs": [
                    {
                        "name": "tree_image",
                        "type": "png",
                        "file": "Tree_visualisation_mqc.png",
                        "description": "Tree visualisation"
                    }
                ],
                "options": [
                    {
                        "name": "ggtree_draw_tree_tree_file",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to Newick tree file"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "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: ggtree_draw_tree ,\n  name: ggtree draw tree,\n  article: \"abs\/10.1002\/cpbi.96\",\n  website: \"https:\/\/yulab-smu.top\/treedata-book\/\",\n  git: \"https:\/\/github.com\/YuLab-SMU\/ggtree\",\n  description: \"R package for visualization of phylogenetic trees with their annotation data\",\n  version: \"3.6.0\",\n  documentation: \"https:\/\/yulab-smu.top\/treedata-book\/\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: ggtree_draw_tree,\n        cname: \"ggtree draw tree\",\n        command: \"Rscript\",\n        category: \"phylogenetics\",\n        output_dir: ggtree_draw_tree,\n        inputs: [\n          { name: tree_file, type: \"newick\", file: \"\", description: \"Newick tree file\" , from: \"parameter\"},\n          { name: popmap, type: \"popmap\" }\n        ],\n        outputs:\n          [\n            { name: tree_image, type: \"png\", file: \"Tree_visualisation_mqc.png\", description: \"Tree visualisation\" },\n          ],\n        options:\n          [\n            {\n              name: ggtree_draw_tree_tree_file,\n              type: input_file,\n              value: \"\",\n              label: \"Path to Newick tree file\",\n            },\n          ],\n      },\n    ],\n  install: {\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     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"
    }
]