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velvetgAppAst.json
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{
"name": "rb-velvetg-stampede",
"parallelism": "PARALLEL",
"version": "1.2.08",
"revision": 2,
"helpURI": "http://www.ebi.ac.uk/~zerbino/velvet/",
"label": "Velvetg",
"shortDescription": "Velvetg, second step of genome assembly",
"longDescription": "Genome assembler for short sequencing reads, second stage.",
"author": "Roger Barthelson",
"datePublished": "08/21/15",
"tags": [
"assembler",
"NGS",
"Illumina",
"454",
"EBI"
],
"ontology": [
"http://sswapmeet.sswap.info/sequenceServices/SequenceServices"
],
"defaultMaxRunTime": "47:56:00",
"defaultQueue": "largemem",
"defaultNodeCount": 1,
"defaultMemoryPerNode": 999,
"defaultProcessorsPerNode": 32,
"executionHost": "rogerab-stampedesville",
"executionSystem": "rogerab-stampedesville",
"executionType": "HPC",
"deploymentPath": "rogerab/applications/velvetg-stmp-1.2.08/bin",
"templatePath": "velvetg_wrapperAst.sh",
"testPath": "../test/velvetg_wrapper_testA.sh",
"checkpointable": true,
"modules": [
"purge",
"load TACC",
"load irods",
"load velvet/1.2.08"
],
"inputs": [
{
"id": "velvet_dir",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": true
},
"details": {
"label": "Output directory from Velveth (VelvetOut.tar.gz)",
"description": "tar archive of velveth output directory"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"text"
]
}
}
],
"parameters": [
{
"id": "read_trkg",
"value": {
"default": "no",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 1
},
"details": {
"label": "Read tracking option, yes or no. Default=no",
"description": "Enter yes to turn on read tracking",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "min_contig_lgth",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 2
},
"details": {
"label": "minimum contig size",
"description": "Enter a number, to set specific minimum contig size",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ctff",
"value": {
"default": "auto",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 3
},
"details": {
"label": "Coverage cutoff value-floating-point or auto",
"description": "Enter a value to set the coverage cutoff manually",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "exp_cov",
"value": {
"default": "auto",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 4
},
"details": {
"label": "Exp. cov. (floating point or auto. Calc. from the coverage)",
"description": "Set a specific expected coverage value",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "long_cov_cutoff",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 5
},
"details": {
"label": "Remove nodes with low long-read coverage AFTER tour bus",
"description": "Enter a floating point to set the long coverage cutoff",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 6
},
"details": {
"label": "Insert size for short paired reads (integer)",
"description": "insert size or paired-end spacing (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length_sd",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 7
},
"details": {
"label": "SD for insert size for short paired reads (integer)",
"description": "Estimated std deviation in the insert size (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length2",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 8
},
"details": {
"label": "Insert size for short paired reads 2 (integer)",
"description": "insert size or paired-end spacing (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length2_sd",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 9
},
"details": {
"label": "SD for insert size for short paired reads 2",
"description": "Estimated std deviation in the insert size (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length_long",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 10
},
"details": {
"label": "Insert size for long paired reads",
"description": "Insert size for long paired reads (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "ins_length_long_sd",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 11
},
"details": {
"label": "SD for insert size for long paired reads",
"description": "Estimated std deviation in the insert size",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "scaffolding",
"value": {
"default": "yes",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 12
},
"details": {
"label": "Scaffolding, yes or no.",
"description": "Enter no to turn off scaffolding",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "max_branch_length",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 13
},
"details": {
"label": "Max length in base pairs of bubble (default: 100)",
"description": "Enter a new branch length (bp).",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "long_mult_cutoff",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 14
},
"details": {
"label": "Min number of long reads required to merge contigs (default: 2)",
"description": "Enter a new cutoff value (integer)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "unused_reads",
"value": {
"default": "no",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 15
},
"details": {
"label": "Export unused reads, yes or no (default: no)",
"description": "Enter yes to export unused to a file",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "alignments",
"value": {
"default": "no",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 16
},
"details": {
"label": "Export a summary of contig alignments (default: no)",
"description": "Enter yes to export summary of contig alignments to a reference",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "exportFiltered",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 17
},
"details": {
"label": "export the long nodes which were eliminated (default: no)",
"description": "Enter yes to export the eliminated nodes to a file",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "paired_exp_fraction",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 18
},
"details": {
"label": "Remove paired connections with a low fraction of the counts",
"description": "Enter a new fraction of counts (default: 0.1)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "conserveLong",
"value": {
"default": "no",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 19
},
"details": {
"label": "preserve sequences with long reads in them (default no)",
"description": "Enter yes to preserve the sequences assembled from long reads",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
}
],
"outputs": [
{
"id": "VelvetgOutput",
"details": {
"label": "Output File",
"description": "The name of the output file."
},
"semantics": {
"ontology": [],
"minCardinality": 1,
"maxCardinality": 1,
"fileTypes": [
"TEXT-0"
]
},
"value": {
"default": "VelvetG_Out.tar.gz",
"required": true,
"type": "string",
"visible": false
}
}
]
}