Runs InterProScan on batches of sequences to retrieve functional annotations.

Workflow: Runs InterProScan on batches of sequences to retrieve functional annotations.

Fetched 2023-01-13 02:47:22 GMT

Verified with cwltool version 3.1.20221201130942

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

ID	Type	Title	Doc
seqtype	https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/workflows/InterProScan-v5-chunked-wf.cwl#seqtype/seqtype (Optional)	Sequence type	Optional, the type of the input sequences (dna/rna (n) or protein (p)). The default sequence type is protein.
databases	Directory
inputFile	File [FASTA]	Input file path	Optional, path to fasta file that should be loaded on Master startup. Alternatively, in CONVERT mode, the InterProScan 5 XML file to convert.
chunk_size	Integer (Optional)
applications	https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/tools/InterProScan/InterProScan-apps.yaml#apps[] (Optional)	Analysis	Optional, comma separated list of analyses. If this option is not set, ALL analyses will be run.
outputFormat	https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/tools/InterProScan/InterProScan-protein_formats.yaml#protein_formats[] (Optional)	output format	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.
catOutputFileName	String
disableResidueAnnotation	Boolean (Optional)	Disables residue annotation	Optional, excludes sites from the XML, JSON output.

ID	Runs	Label	Doc
split_seqs	../utils/fasta_chunker.cwl (CommandLineTool)	split FASTA by number of records	based upon code by developers from EMBL-EBI
combine_interproscan_results	../utils/concatenate.cwl (CommandLineTool)	Redirecting Multiple Files Contain in a Single File	The cat (short for “concatenate“) command is one of the most frequently used command in Linux/Unix like operating systems. cat command allows us to create single or multiple files, view contain of file, concatenate files and redirect output in terminal or files.

ID	Type	Label	Doc
i5Annotations	File

Permalink: https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/workflows/InterProScan-v5-chunked-wf.cwl