mafft.json

{
    "name": "rb-Mafft",
    "parallelism": "SERIAL",
    "version": "7.0.17",
    "helpURI": "http://mafft.cbrc.jp/alignment/software/manual/manual.html",
    "label": "Mafft",
    "shortDescription": "Mafft, multi-sequence aligner",
    "longDescription": "A very, very basic version of Mafft",
    "author": "Roger Barthelson",
    "datePublished": "09/24/15",
    "tags": [
        "aligner",
        "NGS",
        "multi-sequence",
        "rPlant"
    ],
    "ontology": [
        "http://sswapmeet.sswap.info/sequenceServices/SequenceServices"
    ],
    "defaultMaxRunTime": "23:56:00",
    "defaultQueue": "normal",
    "defaultNodeCount": 1,
    "defaultMemoryPerNode": 32,
    "defaultProcessorsPerNode": 16,
    "executionHost": "rogerab-stampedesville",
    "executionSystem": "rogerab-stampedesville",
    "executionType": "HPC",
    "deploymentPath": "rogerab/applications/mafft/bin",
    "templatePath": "mafft_wrapper.sh",
    "testPath": "../test/mafftrun.sh",
    "checkpointable": false,
    "modules": [
        "purge",
        "load TACC",
        "load mafft/7.017"
    ],
    "inputs": [
        {
            "id": "input_seq",
            "value": {
                "default": "",
                "validator": "",
                "visible": true,
                "required": true,
                "order": 1
            },
            "details": {
                "label": "Input sequences",
                "description": "fasta format sequence file"
            },
            "semantics": {
                "ontology": [
                    "http://sswapmeet.sswap.info/sequence/FASTA"
                ],
                "minCardinality": 1,
                "fileTypes": [
                    "fasta-0"
                ]
            }
        }
    ],
    "outputs": [
        {
            "id": "mafft_out.fa",
            "details": {
                "label": "Mafft output file",
                "description": "The output file."
            },
            "semantics": {
                "ontology": [],
                "minCardinality": 1,
                "maxCardinality": 1,
                "fileTypes": [
                    "TEXT-0"
                ]
            },
            "value": {
                "default": "mafft_out.fa",
                "required": true,
                "type": "string",
                "visible": false
            }
        }
    ]
}