[
    {
        "id": "salmon_quant",
        "name": "Salmon quant",
        "article": "10.1038\/nmeth.4197",
        "website": "https:\/\/combine-lab.github.io\/salmon\/",
        "git": "https:\/\/github.com\/COMBINE-lab\/salmon",
        "description": "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. ",
        "version": "1.10.2",
        "documentation": "https:\/\/salmon.readthedocs.io\/en\/latest\/",
        "multiqc": "salmon",
        "sample": true,
        "commands": [
            {
                "name": "salmon_quant_SE",
                "cname": "Salmon quant SE",
                "command": "salmon quant",
                "category": "quantification",
                "output_dir": "salmon\/quant",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "salmon_index",
                        "file": "index",
                        "description": "Index Salmon"
                    }
                ],
                "outputs": [
                    {
                        "name": "lib_counts",
                        "type": "json",
                        "file": "salmon\/quant\/{sample}\/lib_format_counts.json",
                        "description": "Comptages au format JSON"
                    },
                    {
                        "name": "counts",
                        "type": "sf",
                        "file": "salmon\/quant\/{sample}\/quant.sf",
                        "description": "Fichier de compte Salmon"
                    },
                    {
                        "name": "run_info",
                        "type": "json",
                        "file": "salmon\/quant\/{sample}\/cmd_info.json",
                        "description": "Informations sur l'ex\u00e9cution"
                    }
                ],
                "options": [
                    {
                        "name": "salmon_quant_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            },
            {
                "name": "salmon_quant_PE",
                "cname": "Salmon quant PE",
                "command": "salmon quant",
                "category": "quantification",
                "output_dir": "salmon\/quant",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "salmon_index",
                        "file": "index",
                        "description": "Index Salmon"
                    }
                ],
                "outputs": [
                    {
                        "name": "lib_counts",
                        "type": "json",
                        "file": "salmon\/quant\/{sample}\/lib_format_counts.json",
                        "description": "Comptages au format JSON"
                    },
                    {
                        "name": "counts",
                        "type": "sf",
                        "file": "salmon\/quant\/{sample}\/quant.sf",
                        "description": "Fichier de compte Salmon"
                    },
                    {
                        "name": "run_info",
                        "type": "json",
                        "file": "salmon\/quant\/{sample}\/cmd_info.json",
                        "description": "Informations sur l'ex\u00e9cution"
                    }
                ],
                "options": [
                    {
                        "name": "salmon_quant_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "salmon": [
                "Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417-419 (2017). https:\/\/doi.org\/10.1038\/nmeth.4197"
            ]
        },
        "yaml": "{\n  id: salmon_quant,\n  name: Salmon quant,\n  article: \"10.1038\/nmeth.4197\",\n  website: \"https:\/\/combine-lab.github.io\/salmon\/\",\n  git: \"https:\/\/github.com\/COMBINE-lab\/salmon\",\n  description: \"Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. \",\n  version: \"1.10.2\",\n  documentation: \"https:\/\/salmon.readthedocs.io\/en\/latest\/\",\n  multiqc: \"salmon\",\n  sample: true,\n  commands:\n    [\n      {\n        name: salmon_quant_SE,\n        cname: \"Salmon quant SE\",\n        command: salmon quant,\n        category: \"quantification\",\n        output_dir: salmon\/quant,\n        inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"salmon_index\", file: index, description: \"Index Salmon\"}],\n        outputs:\n          [\n            { name: lib_counts, type: \"json\", file: \"salmon\/quant\/{sample}\/lib_format_counts.json\", description: \"Comptages au format JSON\" },\n            { name: counts, type: \"sf\", file: \"salmon\/quant\/{sample}\/quant.sf\", description: \"Fichier de compte Salmon\" },\n            { name: run_info, type: \"json\", file: \"salmon\/quant\/{sample}\/cmd_info.json\", description: \"Informations sur l'ex\u00e9cution\" },\n          ],\n        options:\n          [\n            {\n              name: salmon_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      },\n      {\n        name: salmon_quant_PE,\n        cname: \"Salmon quant PE\",\n        command: salmon quant,\n        category: \"quantification\",\n        output_dir: salmon\/quant,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"salmon_index\", file: index, description: \"Index Salmon\"}],\n        outputs:\n          [\n            { name: lib_counts, type: \"json\", file: \"salmon\/quant\/{sample}\/lib_format_counts.json\", description: \"Comptages au format JSON\" },\n            { name: counts, type: \"sf\", file: \"salmon\/quant\/{sample}\/quant.sf\", description: \"Fichier de compte Salmon\" },\n            { name: run_info, type: \"json\", file: \"salmon\/quant\/{sample}\/cmd_info.json\", description: \"Informations sur l'ex\u00e9cution\" },\n          ],\n        options:\n          [\n            {\n              name: salmon_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      },\n    ],\n  install: {\n    # salmon: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/COMBINE-lab\/salmon\/releases\/download\/v1.3.0\/salmon-1.3.0_linux_x86_64.tar.gz\",\n    #   \"tar -zxvf salmon-1.3.0_linux_x86_64.tar.gz\",\n    #   \"cd bin && ln -s ..\/salmon-latest_linux_x86_64\/bin\/salmon salmon\",\n    #   \"cd .. && rm -r salmon-1.3.0_linux_x86_64.tar.gz salmon-latest_linux_x86_64\/sample_data.tgz\"\n    # ]\n  },\n  citations:  {\n    salmon: [\n      \"Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417-419 (2017). https:\/\/doi.org\/10.1038\/nmeth.4197\"\n    ]\n  }\n}\n"
    }
]