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insilicodb.config
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insilicodb.config
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{
"parameters": [
{
"name": "test-text",
"type": "StringParameter",
"description": "a test to validate strings"
},
// index
{
"name": "index.kmer-size",
"type": "IntegerParameter",
"description": "k-mer (odd) length (default: 31, max value: 31)"
},
{
"name": "index.make-unique",
"type": "BooleanParameter",
"description": "Replace repeated target names with unique names"
}
{
"name": "index.files",
"type": "FilesParameter",
"description": "FASTA files",
"required": true
},
// quant
{
"name": "quant.index",
"type": "FileParameter",
"description": "Filename for the kallisto index to be used for quantification"
},
{
"name": "quant.files",
"type": "FilesParameter",
"description": "FASTQ files",
"required": true
},
{
"name": "quant.bias",
"type": "BooleanParameter",
"description": "Perform sequence based bias correction"
},
{
"name": "quant.bootstrap-samples",
"type": "IntegerParameter",
"description": "Number of bootstrap samples (default: 0)"
},
{
"name": "quant.seed",
"type": "IntegerParameter",
"description": "Seed for the bootstrap sampling (default: 42)"
},
{
"name": "quant.single",
"type": "BooleanParameter",
"description": "Quantify single-end reads"
},
{
"name": "quant.fragment-length",
"type": "DoubleParameter",
"description": "Estimated average fragment length"
},
{
"name": "quant.standard-deviation",
"type": "DoubleParameter",
"description": "Estimated standard deviation of fragment length (default: value is estimated from the input data)"
},
{
"name": "quant.threads",
"type": "IntegerParameter",
"description": "Number of threads to use (default: 1)"
},
{
"name": "quant.pseudobam",
"type": "BooleanParameter",
"description": "Output pseudoalignments in SAM format to stdout"
}
]
}