[
    {
        "id": "radsex_map",
        "name": "radsex_map",
        "article": "https:\/\/doi.org\/10.1111\/1755-0998.13360",
        "website": "https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/1755-0998.13360",
        "git": "https:\/\/github.com\/SexGenomicsToolkit\/radsex",
        "description": "Aligning markers to a genome and computing bias and probability of association with group for each aligned marker",
        "version": "latest",
        "documentation": "https:\/\/sexgenomicstoolkit.github.io\/html\/radsex\/introduction.html",
        "multiqc": "custom",
        "commands": [
            {
                "name": "radsex_map",
                "command": "\/opt\/biotools\/radsex\/bin\/radsex map",
                "category": "radsex",
                "output_dir": "radsex_map",
                "inputs": [
                    {
                        "name": "markers_table",
                        "type": "tsv",
                        "file": "",
                        "description": "Table containing the depth of each marker in each individual (tabulated file)"
                    },
                    {
                        "name": "popmap_file",
                        "type": "popmap",
                        "file": "",
                        "description": "Path to population tsv file"
                    },
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "file": "",
                        "description": "Fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "map_results",
                        "type": "tsv",
                        "file": "map_results.tsv",
                        "description": "Alignment results indicating contig and contig position where the marker was mapped"
                    },
                    {
                        "name": "signi_map_results",
                        "type": "tsv",
                        "file": "map_results.tsv",
                        "description": "results filtered for significant Alignments "
                    }
                ],
                "options": [
                    {
                        "name": "radsex_map_genome_fasta",
                        "prefix": "--genome-file",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to the genome file"
                    },
                    {
                        "name": "radsex_map_chromosome_file",
                        "prefix": "",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to the chromosome file"
                    },
                    {
                        "name": "radsex_map_annotations",
                        "type": "input_file",
                        "value": "",
                        "label": "Annotation file (gtf or gff) : "
                    },
                    {
                        "name": "radsex_map_min_quality",
                        "prefix": "--min-quality",
                        "value": 20,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum mapping quality to consider a marker properly aligned",
                        "type": "numeric"
                    },
                    {
                        "name": "radsex_map_min_frequency",
                        "prefix": "--min-frequency",
                        "value": 0.1,
                        "min": 0,
                        "max": 1,
                        "step": 0.1,
                        "label": "Minimum frequency of a marker in a population to retain it",
                        "type": "numeric"
                    },
                    {
                        "name": "radsex_map_min_depth",
                        "prefix": "--min-depth",
                        "value": 5,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum depth to consider a marker present in an individual",
                        "type": "numeric"
                    },
                    {
                        "name": "radsex_map_signif_threshold",
                        "prefix": "--signif-threshold",
                        "value": 0.05,
                        "min": 0,
                        "max": 1,
                        "step": 0.001,
                        "label": "P-value threshold to consider a marker significantly associated with a phenotypic group",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "prepare_report_script": "radsex_map.prepare.report.R",
        "prepare_report_outputs": [
            "Marker_depth_radsex_map_mqc.png"
        ],
        "install": {
            "radsex_apt_dependencies": [
                "apt-get update",
                "apt-get install -y gcc zlib1g-dev pkg-config libfreetype6-dev libpng-dev"
            ],
            "radsex": [
                "cd \/opt\/biotools",
                "git clone https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/radsex",
                "cd radsex",
                "make -j 10"
            ],
            "sgtr": [
                "Rscript -e 'devtools::install_github(\"SexGenomicsToolkit\/sgtr\");library(\"sgtr\")'"
            ],
            "bedtools": [
                "wget https:\/\/github.com\/arq5x\/bedtools2\/releases\/download\/v2.30.0\/bedtools.static.binary",
                "mv bedtools.static.binary \/opt\/biotools\/bin\/bedtools ",
                "chmod a+x \/opt\/biotools\/bin\/bedtools"
            ]
        },
        "citations": {
            "radsex": [
                "Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., et al. (2021), RADSex: A computational workflow to study sex determination using restriction site\u2010associated DNA sequencing data. Mol Ecol Resour. https:\/\/doi.org\/10.1111\/1755-0998.13360"
            ]
        },
        "yaml": "{\n  id: radsex_map,\n  name: radsex_map,\n  article:  \"https:\/\/doi.org\/10.1111\/1755-0998.13360\",\n  website: \"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/1755-0998.13360\",\n  git: \"https:\/\/github.com\/SexGenomicsToolkit\/radsex\",\n  description: \"Aligning markers to a genome and computing bias and probability of association with group for each aligned marker\",\n  version: \"latest\",\n  documentation: \"https:\/\/sexgenomicstoolkit.github.io\/html\/radsex\/introduction.html\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: radsex_map,\n        command: \/opt\/biotools\/radsex\/bin\/radsex map,\n        category: \"radsex\",\n        output_dir: radsex_map,\n        inputs: [\n          { name: \"markers_table\", type: \"tsv\", file: \"\", description: \"Table containing the depth of each marker in each individual (tabulated file)\" },\n          { name: \"popmap_file\", type: \"popmap\",  file: \"\", description: \"Path to population tsv file\" },\n          { name: \"genome_fasta\", type: \"contigs\", file: \"\", description: \"Fasta reference\"},\n        ],\n        outputs:\n          [\n            { name: map_results, type: \"tsv\", file: \"map_results.tsv\", description: \"Alignment results indicating contig and contig position where the marker was mapped\" },\n            { name: signi_map_results, type: \"tsv\", file: \"map_results.tsv\", description: \"results filtered for significant Alignments \" }\n\n          ],\n        options:\n          [\n             {\n              name: radsex_map_genome_fasta,\n              prefix: \"--genome-file\",\n              type: input_file,\n              value: \"\",\n              label: \"Path to the genome file\",\n            },\n            {\n              name: radsex_map_chromosome_file,\n              prefix: \"\",\n              type: input_file,\n              value: \"\",\n              label: \"Path to the chromosome file\",\n            },\n            {\n              name: \"radsex_map_annotations\",\n              type: \"input_file\",\n              value: \"\",\n              label: \"Annotation file (gtf or gff) : \",\n            },            \n            {\n              name: \"radsex_map_min_quality\",\n              prefix: \"--min-quality\",\n              value: 20,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Minimum mapping quality to consider a marker properly aligned\",\n              type: \"numeric\",\n            },\n            {\n              name: \"radsex_map_min_frequency\",\n              prefix: \"--min-frequency\",\n              value: 0.1,\n              min: 0,\n              max: 1,\n              step: 0.1,\n              label: \"Minimum frequency of a marker in a population to retain it\",\n              type: \"numeric\",\n            },\n            {\n              name: \"radsex_map_min_depth\",\n              prefix: \"--min-depth\",\n              value: 5,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Minimum depth to consider a marker present in an individual\",\n              type: \"numeric\",\n            },\n            {\n              name: \"radsex_map_signif_threshold\",\n              prefix: \"--signif-threshold\",\n              value: 0.05,\n              min: 0,\n              max: 1,\n              step: 0.001,\n              label: \"P-value threshold to consider a marker significantly associated with a phenotypic group\",\n              type: \"numeric\",\n            },\n          ],\n      },\n    ],\n  prepare_report_script:  radsex_map.prepare.report.R,\n  prepare_report_outputs: [\n    Marker_depth_radsex_map_mqc.png,\n  ],\n  install:\n    {\n      radsex_apt_dependencies: [\n        \"apt-get update\",\n        \"apt-get install -y gcc zlib1g-dev pkg-config libfreetype6-dev libpng-dev\"\n      ],\n      radsex: [\n        \"cd \/opt\/biotools\",\n        \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/radsex\",\n        \"cd radsex\",\n        \"make -j 10\",\n      ],\n      sgtr: [\n        'Rscript -e ''devtools::install_github(\"SexGenomicsToolkit\/sgtr\");library(\"sgtr\")'''\n      ],\n      bedtools: [\n        \"wget https:\/\/github.com\/arq5x\/bedtools2\/releases\/download\/v2.30.0\/bedtools.static.binary\",\n        \"mv bedtools.static.binary \/opt\/biotools\/bin\/bedtools \",\n        \"chmod a+x \/opt\/biotools\/bin\/bedtools\",\n      ],\n    },\n    citations:  {\n      radsex: [\n        \"Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., et al. (2021), RADSex: A computational workflow to study sex determination using restriction site\u2010associated DNA sequencing data. Mol Ecol Resour. https:\/\/doi.org\/10.1111\/1755-0998.13360\"\n      ]\n    }\n}\n"
    }
]