[
    {
        "id": "smudgeplotJelly",
        "name": "smudgeplotJelly",
        "article": "https:\/\/doi.org\/10.1038\/s41467-020-14998-3",
        "website": "https:\/\/github.com\/KamilSJaron\/smudgeplot\/wiki",
        "git": "https:\/\/github.com\/KamilSJaron\/smudgeplot",
        "description": "Tool intended for genome profiling (assembly-less understanding of genomes from sequencing reads) in combo with Genomescope",
        "version": "0.2.5",
        "documentation": "https:\/\/github.com\/KamilSJaron\/smudgeplot\/wiki",
        "multiqc": "custom",
        "commands": [
            {
                "name": "smudgeplotJelly",
                "cname": "smudgeplotJelly",
                "command": "smudgeplot.py",
                "category": "quantification",
                "output_dir": "smudgeplotJelly",
                "inputs": [
                    {
                        "name": "kmer_histo",
                        "type": "hist",
                        "description": "kmer counts histogram"
                    },
                    {
                        "name": "jelly_db",
                        "type": "jellyfishcounts",
                        "description": "JellyFish database of kmer counts"
                    }
                ],
                "outputs": [
                    {
                        "name": "smudgeplot",
                        "type": "png",
                        "file": "smudgeplot_mqc.png",
                        "description": "smudgeplot plot "
                    },
                    {
                        "name": "smudgeplotlog",
                        "type": "png",
                        "file": "smudgeplot_log10_mqc.png",
                        "description": "log transform smudgeplot plot "
                    }
                ],
                "options": [
                    {
                        "name": "smudgeplotJelly_kmer_len",
                        "prefix": "-k",
                        "type": "numeric",
                        "value": 21,
                        "min": 1,
                        "max": 256,
                        "step": 1,
                        "label": "K-mers length"
                    },
                    {
                        "name": "smudgeplotJelly_L",
                        "prefix": "-L",
                        "type": "numeric",
                        "value": -1,
                        "min": -1,
                        "max": 500,
                        "step": 1,
                        "label": "Lowercoverage threshold. if -1 use smudgeplot cutoff approximate estimation "
                    },
                    {
                        "name": "smudgeplotJelly_U",
                        "prefix": "-U",
                        "type": "numeric",
                        "value": -1,
                        "min": -1,
                        "max": 5000,
                        "step": 1,
                        "label": "Upper coverage threshold. if -1 use smudgeplot cutoff approximate estimation "
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "jellyfish": [
                "Guillaume Mar\u00e7ais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, Volume 27, Issue 6, 15 March 2011, Pages 764-770, https:\/\/doi.org\/10.1093\/bioinformatics\/btr011"
            ],
            "Smudgeplot": [
                "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)."
            ]
        },
        "yaml": "{\n  id: smudgeplotJelly,\n  name: smudgeplotJelly,\n  article: \"https:\/\/doi.org\/10.1038\/s41467-020-14998-3\",\n  website: \"https:\/\/github.com\/KamilSJaron\/smudgeplot\/wiki\",\n  git: \"https:\/\/github.com\/KamilSJaron\/smudgeplot\",\n  description: \"Tool intended for genome profiling (assembly-less understanding of genomes from sequencing reads) in combo with Genomescope\",\n  version: \"0.2.5\",\n  documentation: \"https:\/\/github.com\/KamilSJaron\/smudgeplot\/wiki\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: smudgeplotJelly,\n        cname: \"smudgeplotJelly\",\n        command: smudgeplot.py,\n        category: \"quantification\",\n        output_dir: smudgeplotJelly,\n        inputs: [{ name: kmer_histo, type: \"hist\", description: \"kmer counts histogram\"  },\n                 { name: jelly_db, type: jellyfishcounts, description: \"JellyFish database of kmer counts\"}],\n        outputs: [{ name: smudgeplot, type: \"png\", file: smudgeplot_mqc.png, description: \"smudgeplot plot \" },\n        { name: smudgeplotlog, type: \"png\", file: smudgeplot_log10_mqc.png, description: \"log transform smudgeplot plot \" }],\n        options:\n          [\n            {\n              name: smudgeplotJelly_kmer_len,\n              prefix: -k,\n              type: numeric,\n              value: 21,\n              min: 1,\n              max: 256,\n              step: 1,\n              label: \"K-mers length\",\n            },\n            {\n              name: smudgeplotJelly_L,\n              prefix: -L,\n              type: numeric,\n              value: -1,\n              min: -1,\n              max: 500,\n              step: 1,\n              label: \"Lowercoverage threshold. if -1 use smudgeplot cutoff approximate estimation \",\n            },\n            {\n              name: smudgeplotJelly_U,\n              prefix: -U,\n              type: numeric,\n              value: -1,\n              min: -1,\n              max: 5000,\n              step: 1,\n              label: \"Upper coverage threshold. if -1 use smudgeplot cutoff approximate estimation \",\n            },\n          ]\n      },\n    ],\n  install:  {\n    # smudgeplot: [\n    #   #\"conda install -c bioconda smudgeplot\"\n    #   \"cd \/opt\/biotools\/\",\n    #   \"git clone https:\/\/github.com\/KamilSJaron\/smudgeplot\",\n    #   \"cd smudgeplot\",\n    #   \"Rscript -e 'install.packages(\\\"viridis\\\")'\",\n    #   \"Rscript install.R\",\n    #   \"pip3 install -r numpy scipy --upgrade\",\n    #   \"install -C exec\/smudgeplot.py \/usr\/local\/bin\",\n    #   \"install -C exec\/smudgeplot_plot.R \/usr\/local\/bin\",\n    #   \"sed -i \\\"s|\\\\.png'|&,width=1200,height=1200|\\\" \/usr\/local\/bin\/smudgeplot_plot.R\"\n    # ],\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  },\n  citations:  {\n    jellyfish: [\n      \"Guillaume Mar\u00e7ais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, Volume 27, Issue 6, 15 March 2011, Pages 764-770, https:\/\/doi.org\/10.1093\/bioinformatics\/btr011\"\n    ],\n    Smudgeplot: [\"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).\"]\n  }\n}"
    }
]