dxapp.json

{
  "name": "quast",
  "title": "QUAST",
  "summary": "Quality Assessment Tool for Genome Assemblies",
  "dxapi": "1.0.0",
  "version": "1.0.4",
  "inputSpec": [
    {
      "name": "contigs",
      "label": "Contigs",
      "class": "array:file",
      "optional": false
    },
    {
      "name": "reference",
      "label": "Reference genome file",
      "class": "file",
      "optional": true
    },
    {
      "name": "genes",
      "label": "Annotated genes file",
      "class": "file",
      "optional": true
    },
    {
      "name": "operons",
      "label": "Annotated operons file",
      "class": "file",
      "optional": true
    },
    {
      "name": "min_contig",
      "label": "Min contig threshold",
      "class": "int",
      "default": 500,
      "optional": true
    },
    {
      "name": "gene_finding",
      "label": "gene finding",
      "class": "boolean",
      "optional": true
    },
    {
      "name": "eukaryote",
      "label": "Genome is an eukaryote",
      "class": "boolean",
      "optional": true
    },
    {
      "name": "est_ref_length",
      "label": "Estimated reference length",
      "class": "int",
      "optional": true
    },
    {
      "name": "scaffolds",
      "label": "Provided assemblies are scaffolds",
      "class": "boolean",
      "optional": true
    }
  ],
  "outputSpec": [
    {
      "name": "report",
      "label": "Report",
      "class": "record"
    }
  ],
  "runSpec": {
    "interpreter": "python2.7",
    "file": "src/quast.py"
  },
  "categories" : ["Assembly"],
  "details": {
    "contactURL": "http://bioinf.spbau.ru/quast",
    "contactEmail": "quast.support@bioinf.spbau.ru",
    "upstreamAuthor" : "Algorithmic Biology Lab at St. Petersburg Academic University of the Russian Academy of Sciences",
    "upstreamVersion" : "2.2.0",
    "upstreamUrl" : "http://bioinf.spbau.ru/quast",
    "upstreamLicenses" : [ "GPLv2" ],
    "citations" : [
        "doi:10.1093/bioinformatics/btt086"
    ]
  }
}