@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix cwl: .
rdfs:comment "Hub gateway base URL (e.g. http://127.0.0.1:8000). Required when backend=hub." ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
rdfs:comment "Catalog entry `structure_predict` (Model surface, biolm-protocols catalog.json).\nPredicts 3D structure for a set of sequences with a single BioLM structure\nmodel. No protocol orchestration needed - this is a direct\n`biolm model run` call.\n" ;
rdfs:label "Core 1: Structure prediction (ESMFold / Boltz-2)" ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
rdfs:comment "JSON array of {pdb, mean_plddt, ...} records, one per input sequence." ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
rdfs:comment "One of encode, predict, generate, lookup." ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:string .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "FASTA (or CSV/JSON) file of sequences to fold. See examples/structure_predict.job.yml." ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"--progress" ] ;
sld:default false ;
sld:type xsd:boolean .
rdfs:comment "Override batch size for processing (default: auto-detect from schema)." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--batch-size" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "Model slug, e.g. esmfold, esm2-150m, esm1v-all, antifold, protein-mpnn." ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
rdfs:comment "Cheap smoke-test mode: caps batch_size to 1 for a fast, low-cost run." ;
sld:default false ;
sld:type xsd:boolean .
rdfs:comment "FASTA, CSV, JSON, or PDB file of items to run through the model." ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--input"
] ;
sld:type cwl:File .
cwl:valueFrom "$(false)" .
rdfs:comment "Structure model slug: esmfold (primary) or boltz-2 (optional, per catalog.json)." ;
sld:default "esmfold" ;
sld:type xsd:string .
rdfs:comment "JSON array of model response records, one per input item." ;
cwl:outputBinding [ CommandOutputBinding:glob
"result.json" ] ;
sld:type cwl:File .
rdfs:comment "Output format: json, fasta, csv, or pdb." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--format" ] ;
sld:default "json" ;
sld:type xsd:string .
rdfs:comment "BIOLM_TOKEN; omit to use the ambient environment or ~/.biolm/credentials." ;
sld:type xsd:string , sld:null .
rdfs:comment "'platform' (biolm.ai) or 'hub' (route via hub_url / BIOLM_BASE_API_URL)." ;
sld:default "platform" ;
sld:type xsd:string .
rdfs:comment "Input type override (sequence, pdb, context, etc.)." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--type" ] ;
sld:type xsd:string , sld:null .
cwl:valueFrom "predict" .
cwl:source .
rdfs:comment "Hub gateway base URL, required when backend=hub." ;
sld:type xsd:string , sld:null .
rdfs:comment "BIOLM_TOKEN value. Omit to use BIOLM_TOKEN already in the environment or ~/.biolm/credentials." ;
sld:type xsd:string , sld:null .
rdfs:comment "Extra model parameters as a JSON string, e.g. '{\"num_seq_per_target\": 4}'." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--params" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Override input format auto-detection (json, fasta, csv, pdb)." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input-format" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "'platform' (default biolm.ai API) or 'hub' (route model inference via hub_url)." ;
sld:default "platform" ;
sld:type xsd:string .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Thin wrapper around `biolm model run ` from biolm-sdk\n(https://pypi.org/project/biolm-sdk/). Runs a single BioLM model action\n(encode / predict / generate / lookup) over sequences, structures, or\nother records from a file.\n\nBackend switch: when `backend` is `hub`, exports `BIOLM_BASE_API_URL` from\n`hub_url` so model inference (and only model inference) is routed through a\nbiolm-hub gateway (`bh serve`); the default `platform` backend leaves the\nhosted biolm.ai API in place. See the repo README for details.\n" ;
rdfs:label "BioLM model run (CLI)" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:prefix "--output" ;
cwl:valueFrom "result.json"
]
) ;
cwl:baseCommand ( "biolm" "model" "run" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "biolm-sdk" ;
SoftwarePackage:specs
]
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biolm-cwl:latest"
] ;
cwl:inputs , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "BIOLM_TOKEN" ;
EnvironmentDef:envValue "$(inputs.biolm_token ? inputs.biolm_token : \"\")"
] ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "BIOLM_BASE_API_URL" ;
EnvironmentDef:envValue "$(inputs.backend == \"hub\" && inputs.hub_url ? inputs.hub_url : \"\")"
]
] .
cwl:source ;
cwl:valueFrom "$(self ? 1 : null)" .
cwl:source .