cwlVersion: v1.0 class: Workflow $namespaces: edam: 'http://edamontology.org/' s: 'http://schema.org/' label: Runs InterProScan on batches of sequences to retrieve functional annotations. requirements: ScatterFeatureRequirement: {} SchemaDefRequirement: types: - $import: ../tools/InterProScan/InterProScan-apps.yaml - $import: ../tools/InterProScan/InterProScan-protein_formats.yaml inputs: - format: 'edam:format_1929' id: inputFile type: File label: Input file path doc: >- Optional, path to fasta file that should be loaded on Master startup. Alternatively, in CONVERT mode, the InterProScan 5 XML file to convert. - id: applications type: ../tools/InterProScan/InterProScan-apps.yaml#apps[]? label: Analysis doc: >- Optional, comma separated list of analyses. If this option is not set, ALL analyses will be run. - id: outputFormat type: ../tools/InterProScan/InterProScan-protein_formats.yaml#protein_formats[]? label: output format doc: >- Optional, case-insensitive, comma separated list of output formats. Supported formats are TSV, XML, JSON, GFF3, HTML and SVG. Default for protein sequences are TSV, XML and GFF3, or for nucleotide sequences GFF3 and XML. - id: databases type: Directory - id: chunk_size type: int? default: 500 - id: disableResidueAnnotation type: boolean? label: Disables residue annotation doc: 'Optional, excludes sites from the XML, JSON output.' - id: seqtype type: - 'null' - type: enum symbols: - p - n name: seqtype label: Sequence type doc: >- Optional, the type of the input sequences (dna/rna (n) or protein (p)). The default sequence type is protein. - id: catOutputFileName type: string default: full_i5_annotations outputs: - id: i5Annotations type: File outputSource: combine_interproscan_results/result steps: split_seqs: run: ../utils/fasta_chunker.cwl in: seqs: inputFile chunk_size: chunk_size out: [ chunks ] run_interproscan: label: Run InterProScan on chunked sequence files run: ../tools/InterProScan/InterProScan-v5.cwl in: inputFile: split_seqs/chunks applications: applications outputFormat: outputFormat databases: databases disableResidueAnnotation: disableResidueAnnotation scatter: inputFile out: [ i5Annotations ] combine_interproscan_results: run: ../utils/concatenate.cwl in: files: run_interproscan/i5Annotations outputFileName: catOutputFileName out: [ result ] $schemas: - 'http://edamontology.org/EDAM_1.20.owl' - 'https://schema.org/docs/schema_org_rdfa.html' s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute, 2018" s:author: "Maxim Scheremetjew"