[
    {
        "id": "genomescope",
        "name": "GenomeScope",
        "article": "10.1038\/s41467-020-14998-3",
        "website": "http:\/\/genomescope.org\/genomescope2.0",
        "git": "https:\/\/github.com\/tbenavi1\/genomescope2.0",
        "description": "Fast genome analysis from unassembled short reads",
        "version": "2.0.0",
        "documentation": "http:\/\/gif.biotech.iastate.edu\/genomescope",
        "multiqc": "custom",
        "commands": [
            {
                "name": "genomescope",
                "command": "genomescope2",
                "category": "quality",
                "output_dir": "genomescope",
                "inputs": [
                    {
                        "name": "kmer_histo",
                        "type": "hist"
                    }
                ],
                "outputs": [
                    {
                        "name": "linear_plot",
                        "type": "png",
                        "file": "\/linear_plot_mqc.png",
                        "description": "profile graph"
                    },
                    {
                        "name": "log_plot",
                        "type": "png",
                        "file": "\/log_plot_mqc.png",
                        "description": "log scale profile graph"
                    },
                    {
                        "name": "transformed_linear_plot",
                        "type": "png",
                        "file": "\/transformed_linear_plot_mqc.png",
                        "description": "transformed profile graph"
                    },
                    {
                        "name": "transformed_log_plot",
                        "type": "png",
                        "file": "\/transformed_log_plot_mqc.png",
                        "description": "transformed log scale profile graph"
                    },
                    {
                        "name": "Summary",
                        "type": "tsv",
                        "file": "\/GenomeScope_Summary_mqc.tsv",
                        "description": "GenomeScope summary table"
                    }
                ],
                "options": [
                    {
                        "name": "genomescope_kmer_len",
                        "prefix": null,
                        "type": "numeric",
                        "value": 21,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "K-mers length"
                    },
                    {
                        "name": "genomescope_ploidy",
                        "prefix": "-p",
                        "type": "numeric",
                        "value": 2,
                        "min": 1,
                        "max": 6,
                        "step": 1,
                        "label": "ploidy (1, 2, 3, 4, 5, or 6) for model to use [default 2]"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "genomescope": [
                "Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11, 1432 (2020). https:\/\/doi.org\/10.1038\/s41467-020-14998-3",
                "Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz, GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2202-2204, https:\/\/doi.org\/10.1093\/bioinformatics\/btx153"
            ]
        },
        "yaml": "{\n  id: genomescope,\n  name: GenomeScope,\n  article: \"10.1038\/s41467-020-14998-3\",\n  website: \"http:\/\/genomescope.org\/genomescope2.0\",\n  git: \"https:\/\/github.com\/tbenavi1\/genomescope2.0\",\n  description: \"Fast genome analysis from unassembled short reads\",\n  version: \"2.0.0\",\n  documentation: \"http:\/\/gif.biotech.iastate.edu\/genomescope\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: genomescope,\n        command: genomescope2,\n        category: \"quality\",\n        output_dir: genomescope,\n        inputs: [{ name: kmer_histo, type: \"hist\" }],\n        outputs: [\n          { name: linear_plot, type: \"png\", file: \"\/linear_plot_mqc.png\", description: \"profile graph\" },\n          { name: log_plot, type: \"png\", file: \"\/log_plot_mqc.png\", description: \"log scale profile graph\" },\n          { name: transformed_linear_plot, type: \"png\", file: \"\/transformed_linear_plot_mqc.png\", description: \"transformed profile graph\" },\n          { name: transformed_log_plot, type: \"png\", file: \"\/transformed_log_plot_mqc.png\", description: \"transformed log scale profile graph\" },\n          { name: Summary, type: \"tsv\", file: \"\/GenomeScope_Summary_mqc.tsv\", description: \"GenomeScope summary table\" }\n        ],\n        options:\n          [\n            {\n              name: genomescope_kmer_len,\n              prefix: ~,\n              type: numeric,\n              value: 21,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"K-mers length\",\n            },\n            {\n              name: genomescope_ploidy,\n              prefix: \"-p\",\n              type: numeric,\n              value: 2,\n              min: 1,\n              max: 6,\n              step: 1,\n              label: \"ploidy (1, 2, 3, 4, 5, or 6) for model to use [default 2]\",\n            },\n          ]\n      },\n    ],\n  install:  {\n    # jellyfish: [\n    #   \"cd \/opt\/biotools\/bin\",\n    #   \"wget -O jellyfish https:\/\/github.com\/gmarcais\/Jellyfish\/releases\/download\/v2.3.0\/jellyfish-linux\",\n    #   \"chmod +x \/opt\/biotools\/bin\/jellyfish\"\n    # ],\n    # genomescope: [\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone https:\/\/github.com\/tbenavi1\/genomescope2.0.git\",\n    #   \"cd genomescope2.0\",\n    #   'Rscript -e ''install.packages(c(\"minpack.lm\",\"argparse\"), repos = \"http:\/\/cran.us.r-project.org\")'' ',\n    #   'Rscript -e ''install.packages(\".\", repos=NULL, type=\"source\") '' '\n    # ],\n  },\n  citations:  {\n    genomescope: [\n      \"Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11, 1432 (2020). https:\/\/doi.org\/10.1038\/s41467-020-14998-3\",\n      \"Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz, GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2202-2204, https:\/\/doi.org\/10.1093\/bioinformatics\/btx153\"\n    ]\n  }\n}"
    }
]