[
    {
        "id": "kallisto_index",
        "name": "kallisto index",
        "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_index",
                "cname": "Kallisto index",
                "command": "kallisto index",
                "category": "indexing",
                "output_dir": "kallisto\/index",
                "inputs": [
                    {
                        "name": "transcriptome_fasta",
                        "type": "contigs",
                        "description": "Transcriptome fasta reference",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "kallisto_index",
                        "file": "index.kidx",
                        "description": "Index kallisto"
                    }
                ],
                "options": [
                    {
                        "name": "kallisto_index_transcriptome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Reference fasta file"
                    }
                ]
            }
        ],
        "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_index,\n  name: kallisto index,\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_index,\n        cname: \"Kallisto index\",\n        command: kallisto index,\n        category: \"indexing\",\n        output_dir: kallisto\/index,\n        inputs: [{ name: transcriptome_fasta, type: \"contigs\", description: \"Transcriptome fasta reference\", from: \"parameter\" }],\n        outputs: [{ name: index, type: \"kallisto_index\", file: index.kidx, description: \"Index kallisto\" }],\n        options:\n          [\n            {\n              name: kallisto_index_transcriptome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Reference fasta file\",\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_linux-v0.46.2\/kallisto bin\",\n      #   \"rm -r kallisto_linux-v0.46.2.tar.gz kallisto_linux-v0.46.2\"\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}"
    }
]