ray_stampede.json

{
  "name": "rb-Ray",
  "version": "2.3.1",
  "helpURI": "http://www.ebi.ac.uk/~zerbino/velvet/",
  "label": "Ray",
  "defaultQueue": "largemem",
  "defaultNodeCount": 1,
  "defaultMemoryPerNode": 999,
  "defaultProcessorsPerNode": 32,
  "defaultMaxRunTime": "47:56:00",
  "defaultRequestedTime": "48:00:00",
  "shortDescription": "Ray, parallel assembler 2.3",
  "longDescription": "Genome assembler for short sequencing reads.",
  "executionSystem": "rogerab-stampedesville",
  "executionType": "HPC",
  "parallelism": "PARALLEL",
  "deploymentPath": "rogerab/applications/Ray2.3/bin",
  "templatePath": "ray_wrapperv2.sh",
  "testPath": "../test/ray_testwrapper.sh",
  "checkpointable": false,
  "tags": [
    "assembler",
    "NGS",
    "Illumina",
    "454",
    "de novo"
  ],
  "modules": [
    "purge",
    "load TACC",
    "load irods",
    "load intel",
    "load mvapich2"
  ],
  "inputs": [
    {
      "id": "seqFolder",
      "details": {
        "label": "Input a folder of sequences to assemble:",
        "description": "Folder of sequence files in fastq, fasta, or sam format",
        "showAttribute": false
      },
      "semantics": {
        "minCardinality": 1,
        "ontology": [
          "http://sswapmeet.sswap.info/sequence/FASTA"
        ],
        "fileTypes": [
          "fasta-0"
        ]
      },
      "value": {
        "default": "",
        "required": true,
        "visible": true
      }
    }
  ],
  "parameters": [
    {
      "id": "interleaved",
      "details": {
        "label": "interleaved pairs",
        "description": "Are your paired files in interleaved format?",
        "showAttribute": false
      },
      "semantics": {
        "ontology": [
          "xs:string"
        ]
      },
      "value": {
        		"type": "enumeration",
                "default": "",
                "enum_values": [
                    { "": "files are not interleaved pairs" },
                    { "yes": "paired files are in interleaved format" }
                ],
                "visible": true,
        "order": 1
      }
    },
    {
      "id": "kmer",
      "details": {
        "label": "select the kmer size",
        "description": "set the Kmer value for assembly (odd integer)",
        "showAttribute": false
      },
      "semantics": {
        "ontology": [
          "xs:integer"
        ]
      },
      "value": {
        "default": 31,
        "type": "number",
        "validator": "[0-9]+",
        "required": true,
        "visible": true,
        "order": 2
      }
    }
  ],
     "outputs": [
        {
            "id": "Output",
            "details": {
                "label": "RayOutput",
                "description": "The name of the output file."
            },
            "semantics": {
                "ontology": [],
                "minCardinality": 1,
                "fileTypes": [
                    "TEXT-0"
                ]
            },
            "value": {
                "default": "RayOutput",
                "required": true,
                "type": "string",
                "visible": false
            }
        }
    ]
}