[
    {
        "id": "vcftools_allelic_variants_count_sfs",
        "name": "vcftools allelic variants count sfs",
        "description": "VCFtools to count the allele frequency of each variant and convert to partial est-sfs format input.",
        "version": "0.1.16",
        "website": "https:\/\/vcftools.github.io\/index.html",
        "git": "https:\/\/github.com\/vcftools\/vcftools",
        "documentation": "https:\/\/vcftools.github.io\/man_latest.html",
        "article": "http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330",
        "multiqc": "custom",
        "commands": [
            {
                "name": "vcftools_allelic_variants_count_sfs",
                "cname": "vcftools allelic variants count sfs",
                "command": "vcftools",
                "category": "vcf_postprocess",
                "output_dir": "vcf_frq_count",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf_file",
                        "description": "Variant Calling Format (vcf) file"
                    }
                ],
                "outputs": [
                    {
                        "name": "frq",
                        "type": "tsv",
                        "file": "vcf_count.frq.count",
                        "description": "tsv file with allele frequency count"
                    },
                    {
                        "name": "sfs",
                        "type": "sfs",
                        "file": "vcf_count.sfs.count",
                        "description": "vcf with allele frequency count as est-sfs format"
                    }
                ],
                "options": [
                    {
                        "name": "vcftools_allelic_variants_count_sfs_snps_only",
                        "prefix": "--remove-indels",
                        "value": true,
                        "label": "Filter insertion deletion variants",
                        "type": "checkbox"
                    },
                    {
                        "name": "vcftools_allelic_variants_count_sfs_biallelic_only",
                        "prefix": "--min-alleles 2 --max-alleles 2",
                        "value": true,
                        "label": "Filter non biallelic variants",
                        "type": "checkbox"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "vcftools": [
                "The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330"
            ]
        },
        "yaml": "{\n  id: \"vcftools_allelic_variants_count_sfs\",\n  name: \"vcftools allelic variants count sfs\",\n  description: \"VCFtools to count the allele frequency of each variant and convert to partial est-sfs format input.\",\n  version: \"0.1.16\",\n  website: \"https:\/\/vcftools.github.io\/index.html\",\n  git: \"https:\/\/github.com\/vcftools\/vcftools\",\n  documentation: \"https:\/\/vcftools.github.io\/man_latest.html\",\n  article: \"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"vcftools_allelic_variants_count_sfs\",\n        cname: \"vcftools allelic variants count sfs\",\n        command: \"vcftools\",\n        category: vcf_postprocess,\n        output_dir: \"vcf_frq_count\",\n        inputs:\n          [\n            { name: \"vcf\", type: \"vcf_file\", description: \"Variant Calling Format (vcf) file\" },\n          ],\n        outputs:\n          [\n            { name: \"frq\", type: \"tsv\", file: \"vcf_count.frq.count\", description: \"tsv file with allele frequency count\" },\n            { name: \"sfs\", type: \"sfs\", file: \"vcf_count.sfs.count\", description: \"vcf with allele frequency count as est-sfs format\" }\n          ],\n        options:\n          [\n            {\n              name: \"vcftools_allelic_variants_count_sfs_snps_only\",\n              prefix: \"--remove-indels\",\n              value: True,\n              label: \"Filter insertion deletion variants\",\n              type: \"checkbox\",\n            },\n            {\n              name: \"vcftools_allelic_variants_count_sfs_biallelic_only\",\n              prefix: \"--min-alleles 2 --max-alleles 2\",\n              value: True,\n              label: \"Filter non biallelic variants\",\n              type: \"checkbox\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # vcftools: [\n      #   \"apt-get install -y vcftools\"\n      # ]\n    },\n  citations:  {\n    vcftools: [\n      \"The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330\"\n    ],\n  }\n}\n"
    }
]