[
    {
        "id": "sam_to_phylip",
        "name": "SAM to phylip",
        "article": "",
        "website": "",
        "git": "",
        "description": "Conversion of SAM files to phylip format by grouping sample entries by reference sequence",
        "version": "6.6.0",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "sam_to_phylip",
                "command": "",
                "category": "quality",
                "output_dir": "sam_to_phylip",
                "inputs": [
                    {
                        "name": "sams",
                        "type": "sam"
                    }
                ],
                "outputs": [
                    {
                        "name": "phylips",
                        "type": "phylip",
                        "file": "{}.phylip",
                        "description": "phylips files"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "samtools": [
                "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ],
            "emboss": [
                "Rice P., Longden I. and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics. 2000 16(6):276-277"
            ]
        },
        "yaml": "{\n  id: sam_to_phylip,\n  name: SAM to phylip,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"Conversion of SAM files to phylip format by grouping sample entries by reference sequence\",\n  version: \"6.6.0\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: sam_to_phylip,\n        command: \"\",\n        category: \"quality\",\n        output_dir: sam_to_phylip,\n        inputs: [{ name: sams, type: \"sam\" }],\n        outputs: [{ name: phylips, type: \"phylip\", file: \"{}.phylip\", description: \"phylips files\" }],\n        options: [],\n      },\n    ],\n  install:\n    {\n      # samtools:\n      #   [\n      #     \"cd \/opt\/biotools\",\n      #     \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n      #     \"tar -xvjf samtools-1.9.tar.bz2\",\n      #     \"cd samtools-1.9\",\n      #     \".\/configure && make\",\n      #     \"cd ..\",\n      #     \"mv samtools-1.9\/samtools bin\/samtools\",\n      #     \"rm -r samtools-1.9 samtools-1.9.tar.bz2\",\n      #   ],\n      # seqret: [\n      #      \"cd \/opt\/biotools\",\n      #      \"wget ftp:\/\/emboss.open-bio.org\/pub\/EMBOSS\/EMBOSS-6.6.0.tar.gz\",\n      #      \"tar -xvzf EMBOSS-6.6.0.tar.gz\",\n      #      \"cd EMBOSS-6.6.0\",\n      #      \".\/configure --without-x\",\n      #      \"make -j 8\",\n      #      \"cd ..\/bin && ln -s \/opt\/biotools\/EMBOSS-6.6.0\/emboss\/seqret seqret\",\n      #      \"rm ..\/EMBOSS-6.6.0.tar.gz\"\n      #   ],\n    },\n  citations:\n    {\n      samtools:\n        [\n          \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\",\n        ],\n      emboss:\n        [\n          \"Rice P., Longden I. and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics. 2000 16(6):276-277\"\n        ],\n    },\n}\n"
    }
]