{
    "name": "spades",
    "title": "SPAdes Assembler",
    "summary": "De Novo assembler suitable for bacterial single-cell and isolate genomes",
    "dxapi": "1.0.0",
    "version": "1.0.3",
    "inputSpec": [
        {
            "name": "paired_reads",
            "label": "Paired-end reads",
            "class": "array:gtable",
            "type": "LetterReads",
            "optional": true
        },
        {
            "name": "mate_pairs",
            "label": "Mate-pairs",
            "class": "array:gtable",
            "type": "LetterReads",
            "optional": true
        },
        {
            "name": "unpaired_reads",
            "label": "Unpaired reads",
            "class": "array:gtable",
            "type": "LetterReads",
            "optional": true
        },        
        {
            "name": "is_single_cell",
            "label": "Single Cell Dataset",
            "class": "boolean",
            "optional": true,
            "default": false
        },
        {
            "name": "is_only_assembler",
            "label": "Run assembler only",
            "class": "boolean",
            "optional": true,
            "default": false
        },
        {
            "name" : "is_careful_mode",
            "label": "Run assembler in careful mode",
            "class": "boolean",
            "optional": true,
            "default": true
        },
        {
            "name" : "k",
            "label" : "K-mer lengths to use",
            "class" : "string",
            "optional" : true,
            "default" : "21,33,55"
        },
        {
            "name": "memory",
            "label": "Memory limit, in GB",
            "class": "int",
            "optional": true,
            "default": 64
        }
    ],
    "outputSpec": [
        {
            "name": "contigs",
            "label": "Contigs",
            "class": "file"
        },
        {
            "name": "scaffolds",
            "label": "Scaffolds",
            "class": "file"
        }
    ],
    "runSpec": {
        "file": "src/spades-dnanexus.sh",
        "interpreter" : "bash",
        "systemRequirements" : {
            "main" : {
                "instanceType": "dx_m2.4xlarge"
            }
        },
        "buildDepends": [
            {"name": "libz-dev"}
        ]
    },
    "categories" : ["Assembly"],
    "details": {
        "advancedInputs" : [ "k", "memory" ],
        "contactURL": "http://bioinf.spbau.ru/spades",
        "contactEmail": "spades.support@bioinf.spbau.ru",
        "upstreamAuthor" : "Algorithmic Biology Lab at St. Petersburg Academic University of the Russian Academy of Sciences",
        "upstreamVersion" : "2.5.0",
        "upstreamUrl" : "http://bioinf.spbau.ru/spades",
        "upstreamLicenses" : [ "GPLv2" ],
        "citations" : [
            "doi:10.1089/cmb.2012.0021",
            "doi:10.1186/1471-2164-14-S1-S7",
            "doi:10.1007/978-3-642-37195-0_13"
        ]
    }
}
