[
    {
        "id": "KMC",
        "name": "KMC",
        "article": "",
        "website": "http:\/\/sun.aei.polsl.pl\/REFRESH\/index.php?page=projects&project=kmc&subpage=about",
        "git": "https:\/\/github.com\/tbenavi1\/KMC",
        "description": "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ\/FASTA files",
        "version": "3.2.1",
        "documentation": "http:\/\/www.genome.umd.edu\/docs\/JellyfishUserGuide.pdf",
        "multiqc": "custom",
        "commands": [
            {
                "name": "KMC",
                "cname": "KMC",
                "command": "kmc",
                "category": "quantification",
                "output_dir": "KMC",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "kmer_histo",
                        "type": "hist",
                        "file": "kmer_histo_KMC.hist",
                        "description": "KMC kmer counts histogram"
                    },
                    {
                        "name": "kmc_db",
                        "type": "kmcDB",
                        "file": "kmcdb.kmc_suf",
                        "description": "KMC database of kmer counts"
                    }
                ],
                "options": [
                    {
                        "name": "KMC_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "KMC_kmer_len",
                        "prefix": "-k",
                        "type": "numeric",
                        "value": 21,
                        "min": 1,
                        "max": 256,
                        "step": 1,
                        "label": "K-mers length"
                    },
                    {
                        "name": "KMC_mem",
                        "prefix": "-m",
                        "type": "numeric",
                        "value": 2,
                        "min": 1,
                        "max": 256,
                        "step": 1,
                        "label": "approximate amount of RAM to use in GB"
                    },
                    {
                        "name": "KMC_ci",
                        "prefix": "-ci",
                        "type": "numeric",
                        "value": 1,
                        "min": 1,
                        "max": 50,
                        "step": 1,
                        "label": "exclude kmers occurring less than <value> times"
                    },
                    {
                        "name": "KMC_cs",
                        "prefix": "-cs",
                        "type": "numeric",
                        "value": 10000,
                        "min": 1000,
                        "max": 100000,
                        "step": 10,
                        "label": "exclude kmers occurring more than <value> times"
                    },
                    {
                        "name": "KMC_cx",
                        "prefix": "-cx",
                        "type": "numeric",
                        "value": 10000,
                        "min": 1000,
                        "max": 100000,
                        "step": 10,
                        "label": "the maximum value of counter to be stored in the histogram file"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "KMC": [
                "Kokot, M., D\u0142ugosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759-2761"
            ]
        },
        "yaml": "{\n  id: KMC,\n  name: KMC,\n  article: \"\",\n  website: \"http:\/\/sun.aei.polsl.pl\/REFRESH\/index.php?page=projects&project=kmc&subpage=about\",\n  git: \"https:\/\/github.com\/tbenavi1\/KMC\",\n  description: \"KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ\/FASTA files\",\n  version: \"3.2.1\",\n  documentation: \"http:\/\/www.genome.umd.edu\/docs\/JellyfishUserGuide.pdf\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: KMC,\n        cname: \"KMC\",\n        command: kmc,\n        category: \"quantification\",\n        output_dir: KMC,\n        inputs: [{ name: read, type: \"reads\" }],\n        outputs: [\n                  { name: kmer_histo, type: \"hist\", file: kmer_histo_KMC.hist, description: \"KMC kmer counts histogram\" },\n                  { name: kmc_db, type: \"kmcDB\", file: kmcdb.kmc_suf, description: \"KMC database of kmer counts\"}\n                  ],\n        options:\n          [\n            {\n              name: KMC_threads,\n              prefix: -t,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: KMC_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: KMC_mem,\n              prefix: -m,\n              type: numeric,\n              value: 2,\n              min: 1,\n              max: 256,\n              step: 1,\n              label: \"approximate amount of RAM to use in GB\",\n            },\n            {\n              name: KMC_ci,\n              prefix: -ci,\n              type: numeric,\n              value: 1,\n              min: 1,\n              max: 50,\n              step: 1,\n              label: \"exclude kmers occurring less than <value> times\",\n            },\n            {\n              name: KMC_cs,\n              prefix: -cs,\n              type: numeric,\n              value: 10000,\n              min: 1000,\n              max: 100000,\n              step: 10,\n              label: \"exclude kmers occurring more than <value> times\",\n            },\n            {\n              name: KMC_cx,\n              prefix: -cx,\n              type: numeric,\n              value: 10000,\n              min: 1000,\n              max: 100000,\n              step: 10,\n              label: \"the maximum value of counter to be stored in the histogram file\",\n            },\n          ]\n      },\n    ],\n  install:  {\n    # tbenavi1-KMC: [\n    #   \"cd \/opt\/biotools\/\",\n    #   \"git clone https:\/\/github.com\/tbenavi1\/KMC.git\",\n    #   \"cd KMC\",\n    #   \"make -j 8\",\n    #   \"chmod +x bin\/*\",\n    #   \"cp bin\/* \/opt\/biotools\/bin\/ \",\n    #   \"cd ..\",\n    #   \"rm -rf KMC\"\n    # ],\n  },\n  citations:  {\n    KMC: [\"Kokot, M., D\u0142ugosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759-2761\"]\n  }\n}\n"
    }
]