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soap-trans-small.json
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{
"name": "rb-Soapdenovo-trans-small",
"parallelism": "SERIAL",
"version": "1.0.4",
"revision": 4,
"helpURI": "https://pods.iplantcollaborative.org/wiki/display/DEapps/soapdenovo",
"label": "Soapdenovo-trans-small",
"shortDescription": "Soapdenovo_Trans",
"longDescription": "Fast Transcriptome assembler",
"author": "Roger Barthelson",
"datePublished": "06/08/16",
"tags": [
"assembler",
"NGS",
"Illumina",
"BGI"
],
"ontology": [
"http://sswapmeet.sswap.info/sequenceServices/SequenceServices"
],
"defaultMaxRunTime": "47:56:00",
"defaultQueue": "normal",
"defaultNodeCount": 1,
"defaultMemoryPerNode": 64,
"defaultProcessorsPerNode": 24,
"executionSystem": "rogerab-starland",
"executionType": "HPC",
"deploymentPath": "rogerab/applications/soap-trans-1.0.4/bin",
"templatePath": "SoapdenovoTrans_wrapper2.sh",
"testPath": "../test/soaptrans8.sh",
"checkpointable": true,
"modules": [
"purge",
"load TACC"
],
"inputs": [
{
"id": "reads1_1",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": false,
"order": 1
},
"details": {
"label": "Paired Library1, reads1",
"description": "Sequence file in fastq or fasta format"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"fasta-0"
]
}
},
{
"id": "reads1_2",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": false,
"order": 2
},
"details": {
"label": "Paired Library1, reads2",
"description": "Sequence file in fastq or fasta format"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"fasta-0"
]
}
},
{
"id": "reads2_1",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": false,
"order": 3
},
"details": {
"label": "Paired Library2, reads1",
"description": "Sequence file in fastq or fasta format"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"fasta-0"
]
}
},
{
"id": "reads2_2",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": false,
"order": 4
},
"details": {
"label": "Paired Library2, reads2",
"description": "Sequence file in fastq or fasta format"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"fasta-0"
]
}
},
{
"id": "reads5_1",
"value": {
"default": "",
"validator": "",
"visible": true,
"required": false,
"order": 5
},
"details": {
"label": "Single Reads Library",
"description": "Sequence file in fastq or fasta format"
},
"semantics": {
"ontology": [
"http://sswapmeet.sswap.info/sequence/FASTA"
],
"minCardinality": 1,
"fileTypes": [
"fasta-0"
]
}
}
],
"parameters": [
{
"id": "max_rd_len",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": true,
"visible": true,
"order": 1
},
"details": {
"label": "Maximum read length",
"description": "Longest reads used for assembly",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "avg_ins1",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 2
},
"details": {
"label": "Average insert size, library 1",
"description": "Pair spacing (required if there is a library 1)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "reverse_seq1",
"value": {
"default": "0",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 3
},
"details": {
"label": "read orientations, library 1",
"description": "0 for Forward,Reverse, 1 for Reverse,Forward",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "asm_flags1",
"value": {
"default": "3",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 4
},
"details": {
"label": "assembly steps, library 1",
"description": "1 for contig assmbly,2 for scaffolding, 3 for both",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "rank1",
"value": {
"default": "1",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 5
},
"details": {
"label": "order for scaffolding, library 1",
"description": "set order for use in scaffolding",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "format1",
"value": {
"default": "q",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 6
},
"details": {
"label": "file format, library 1, q or a",
"description": "q for fastq, a for fasta",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "avg_ins2",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 7
},
"details": {
"label": "average insert size, library 2",
"description": "Pair spacing (required if there is a library 2)",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "reverse_seq2",
"value": {
"default": "0",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 8
},
"details": {
"label": "read orientations, library 2",
"description": "0 for Forward,Reverse, 1 for Reverse,Forward",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "asm_flags2",
"value": {
"default": "3",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 9
},
"details": {
"label": "assembly steps, library 2",
"description": "1 for contig assmbly,2 for scaffolding, 3 for both",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "rank2",
"value": {
"default": "",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 10
},
"details": {
"label": "order for scaffolding, library 2",
"description": "set order for use in scaffolding",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "format2",
"value": {
"default": "q",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 11
},
"details": {
"label": "file format, library 2, q or a",
"description": "q for fastq, a for fasta",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "asm_flags5",
"value": {
"default": "1",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 12
},
"details": {
"label": "assembly steps, single reads",
"description": "1 for contig assmbly,2 for scaffolding, 3 for both",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "format5",
"value": {
"default": "q",
"type": "string",
"validator": "",
"required": false,
"visible": true,
"order": 13
},
"details": {
"label": "file format, singles, q or a",
"description": "q for fastq, a for fasta",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "kmer",
"value": {
"default": "27",
"type": "string",
"validator": "",
"required": true,
"visible": true,
"order": 14
},
"details": {
"label": "kmer size",
"description": "kmer size",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "mergeLevel",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 15
},
"details": {
"label": "merge level",
"description": "contig merging strength, 0-3",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "dkmers",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 16
},
"details": {
"label": "kmer selection",
"description": "delete kmers with frequency n or less",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "dEdges",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 17
},
"details": {
"label": "edge selection",
"description": "delete edges with coverage of n or less",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "fillGaps",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 18
},
"details": {
"label": "fill gaps in scaffold",
"description": "YES to fill gaps in scaffold",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "maxLocus",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 19
},
"details": {
"label": "maximum number of transcripts per locus",
"description": "default is 5",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "minLen",
"value": {
"default": "",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 20
},
"details": {
"label": "minimum contig length for scaffolding",
"description": "default is 100",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
},
{
"id": "kRange",
"value": {
"default": "127",
"validator": "",
"required": false,
"visible": true,
"type": "string",
"order": 21
},
"details": {
"label": "maximum kmer setting",
"description": "31 or 127",
"visible": true
},
"semantics": {
"ontology": [
"xs:string"
]
}
}
],
"outputs": [
{
"id": "SoapTransOutput",
"details": {
"label": "Output File",
"description": "The name of the output file."
},
"semantics": {
"ontology": [],
"minCardinality": 1,
"fileTypes": [
"TEXT-0"
]
},
"value": {
"default": "SoapTransOut.scafSeq",
"required": true,
"type": "string",
"visible": false
}
}
]
}