[
    {
        "id": "kallisto_quant",
        "name": "kallisto quant",
        "article": "10.1038\/nbt.3519",
        "website": "https:\/\/pachterlab.github.io\/kallisto\/",
        "git": "https:\/\/github.com\/pachterlab\/kallisto",
        "description": "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.",
        "version": "0.48.0",
        "documentation": "https:\/\/pachterlab.github.io\/kallisto\/manual",
        "multiqc": "kallisto",
        "commands": [
            {
                "name": "kallisto_quant_SE",
                "cname": "Kallisto quant SE",
                "command": "kallisto quant",
                "category": "quantification",
                "output_dir": "kallisto\/quant",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "kallisto_index",
                        "file": "index.kidx",
                        "description": "Index kallisto",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "h5",
                        "type": "h5",
                        "file": "{sample}\/abundance.h5",
                        "description": "Abondances au format h5"
                    },
                    {
                        "name": "counts",
                        "type": "tsv",
                        "file": "{sample}\/abundance.tsv",
                        "description": "Table d'abondance"
                    },
                    {
                        "name": "run_info",
                        "type": "json",
                        "file": "{sample}\/run_info.json",
                        "description": "Informations sur l'ex\u00e9cution"
                    }
                ],
                "options": [
                    {
                        "name": "kallisto_quant_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "kallisto_quant_fragment_length_SE",
                        "prefix": "-l",
                        "type": "numeric",
                        "value": 300,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Estimated average fragment length"
                    },
                    {
                        "name": "kallisto_quant_standard_deviation_SE",
                        "prefix": "-s",
                        "type": "numeric",
                        "value": 2,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Estimated standard deviation of fragment length"
                    }
                ]
            },
            {
                "name": "kallisto_quant_PE",
                "cname": "Kallisto quant PE",
                "command": "kallisto quant",
                "category": "quantification",
                "output_dir": "kallisto\/quant",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "kallisto_index",
                        "file": "index.kidx",
                        "description": "Index kallisto",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "h5",
                        "type": "h5",
                        "file": "{sample}\/abundance.h5",
                        "description": "Abondances au format h5"
                    },
                    {
                        "name": "counts",
                        "type": "tsv",
                        "file": "{sample}\/abundance.tsv",
                        "description": "Table d'abondance"
                    },
                    {
                        "name": "run_info",
                        "type": "json",
                        "file": "{sample}\/run_info.json",
                        "description": "Informations sur l'ex\u00e9cution"
                    }
                ],
                "options": [
                    {
                        "name": "kallisto_quant_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "kallisto_quant_stranded_PE",
                        "type": "radio",
                        "choices": [
                            {
                                "Not stranded": ""
                            },
                            {
                                "Forward Reverse": "--fr-stranded"
                            },
                            {
                                "Reverse Forward": "--rf-stranded"
                            }
                        ],
                        "value": "",
                        "label": "For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "kallisto": [
                "Bray, N., Pimentel, H., Melsted, P. et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525-527 (2016). https:\/\/doi.org\/10.1038\/nbt.3519"
            ]
        },
        "yaml": "{\n  id: kallisto_quant,\n  name: kallisto quant,\n  article: \"10.1038\/nbt.3519\",\n  website: \"https:\/\/pachterlab.github.io\/kallisto\/\",\n  git: \"https:\/\/github.com\/pachterlab\/kallisto\",\n  description: \"kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.\",\n  version: \"0.48.0\",\n  documentation: \"https:\/\/pachterlab.github.io\/kallisto\/manual\",\n  multiqc: \"kallisto\",\n  commands:\n    [\n      {\n        name: kallisto_quant_SE,\n        cname: \"Kallisto quant SE\",\n        command: kallisto quant,\n        category: \"quantification\",\n        output_dir: kallisto\/quant,\n        inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"kallisto_index\", file: index.kidx, description: \"Index kallisto\", from: \"parameter\" }],\n        outputs:\n          [\n            { name: h5, type: \"h5\", file: \"{sample}\/abundance.h5\", description: \"Abondances au format h5\" },\n            { name: counts, type: \"tsv\", file: \"{sample}\/abundance.tsv\", description: \"Table d'abondance\" },\n            { name: run_info, type: \"json\", file: \"{sample}\/run_info.json\", description: \"Informations sur l'ex\u00e9cution\" },\n          ],\n        options:\n          [\n            {\n              name: kallisto_quant_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: kallisto_quant_fragment_length_SE,\n              prefix: -l,\n              type: numeric,\n              value: 300,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Estimated average fragment length\",\n            },\n            {\n              name: kallisto_quant_standard_deviation_SE,\n              prefix: -s,\n              type: numeric,\n              value: 2,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Estimated standard deviation of fragment length\",\n            }\n          ],\n      },\n      {\n        name: kallisto_quant_PE,\n        cname: \"Kallisto quant PE\",\n        command: kallisto quant,\n        category: \"quantification\",\n        output_dir: kallisto\/quant,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"kallisto_index\", file: index.kidx, description: \"Index kallisto\", from: \"parameter\" }],\n        outputs:\n          [\n            { name: h5, type: \"h5\", file: \"{sample}\/abundance.h5\", description: \"Abondances au format h5\" },\n            { name: counts, type: \"tsv\", file: \"{sample}\/abundance.tsv\", description: \"Table d'abondance\" },\n            { name: run_info, type: \"json\", file: \"{sample}\/run_info.json\", description: \"Informations sur l'ex\u00e9cution\" },\n          ],\n        options:\n          [\n            {\n              name: kallisto_quant_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: kallisto_quant_stranded_PE,\n              type: radio,\n              choices:\n                [\n                  Not stranded: \"\",\n                  Forward Reverse: --fr-stranded,\n                  Reverse Forward: --rf-stranded,\n                ],\n              value: \"\",\n              label: For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse,\n            },\n          ],\n      }\n    ],\n  install:\n    {\n      # kallisto: [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget https:\/\/github.com\/pachterlab\/kallisto\/releases\/download\/v0.46.2\/kallisto_linux-v0.46.2.tar.gz\",\n      #   \"tar -zxvf kallisto_linux-v0.46.2.tar.gz\",\n      #   \"mv kallisto\/kallisto bin\",\n      #   \"rm -r kallisto_linux-v0.46.2.tar.gz kallisto\"\n      # ]\n    },\n  citations:  {\n    kallisto: [\n      \"Bray, N., Pimentel, H., Melsted, P. et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525-527 (2016). https:\/\/doi.org\/10.1038\/nbt.3519\"\n    ]\n  }\n}"
    }
]