107 lines
3.3 KiB
JSON
107 lines
3.3 KiB
JSON
{
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"params": {
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"fasta_list": {
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"type": "file[]",
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"description": "FASTA files containing protein sequences",
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"default": [],
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.fasta_list",
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"examples": [
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["/omic/olamide/examples/prot1.fasta", "/omic/olamide/examples/prot2.fasta"]
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],
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"pattern": ".*\\.fasta$",
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"validation": {},
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"notes": "Select one or more FASTA files with protein sequences"
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},
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"outdir": {
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"type": "folder",
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"description": "Output Directory",
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"default": "/omic/olamide/output",
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"required": true,
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"pipeline_io": "output",
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"var_name": "params.outdir",
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"examples": [
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"/omic/olamide/output"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Select where to save your analysis results"
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},
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"num_samples": {
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"type": "integer",
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"description": "Number of protein structure samples",
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"default": 10,
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.num_samples",
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"examples": [
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"10"
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],
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"pattern": "^\\d+$",
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"validation": {
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"min": 1
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},
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"notes": "More samples provide better coverage of conformational space"
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},
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"batch_size_100": {
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"type": "integer",
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"description": "Batch size parameter",
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"default": 10,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.batch_size_100",
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"hidden": true,
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"examples": [
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"10"
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],
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"pattern": "^\\d+$"
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},
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"temperature": {
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"type": "integer",
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"description": "Temperature (K) for free energy",
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"default": 300,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.temperature",
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"examples": [
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"300"
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],
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"pattern": "^\\d+$",
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"validation": {
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"min": 200,
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"max": 500
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},
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"notes": "Temperature in Kelvin for free energy calculations"
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},
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"n_clusters": {
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"type": "integer",
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"description": "Number of conformational clusters",
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"default": 5,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.n_clusters",
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"examples": [
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"5"
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],
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"pattern": "^\\d+$",
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"validation": {
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"min": 2
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},
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"notes": "Number of clusters for free energy analysis"
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},
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"cache_dir": {
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"type": "folder",
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"description": "Embeddings cache directory",
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"default": "/tmp/bioemu_cache",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.cache_dir",
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"hidden": true,
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"examples": [
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"/tmp/bioemu_cache"
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]
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}
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}
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}
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