Clustal Omega

Clustal Omega is a fast and scalable tool that makes multiple sequence alignments of protein sequences. For more information, see the tool's homepage.

Function Call

toolchest.clustalo(
    inputs,
    output_path=None,
    tool_args="",
    is_async=False,
)
toolchest$clustalo(
    inputs,
    output_path = NULL,
    tool_args = "",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

Argument

Use in place of:

Description

inputs

-i

Path to a file that will be passed in as input. This can be a local filepath or an AWS S3 URI.

output_path

-o

(optional) File path where the output will be downloaded.
If omitted, skips download. The outputs can be downloaded manually.

tool_args

all other arguments

(optional) Additional arguments to be passed to Clustal Omega. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.

is_async

Whether to run a job asynchronously.

Output Files

For a output_path directory with base name NAME, the Clustal Omega output will be downloaded to output_path/NAME. Two log files (NAME.log and NAME.error.log) will be outputted to the output_path directory.

For example, if output_path is /example/path/name, the following files will be outputted:

/example/path/name
|
--- /example/path/name/name
|
--- /example/path/name/name.log
|
--- /example/path/name/name.error.log

Return Value

This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.

Notes

Amazon AWS S3 inputs

Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.

Async runs

Set the is_async parameter to true if you would like to run a Clustal Omega job asynchronously. See Async Runs for more information.

Tool Versions

Toolchest currently supports version 1.2.4 of Clustal Omega. Every request to run Clustal Omega with Toolchest will default to this version.

Supported Additional Arguments

  • --auto
  • --dealign
  • --infmt
  • --is-profile
  • --iter
  • --iterations
  • --max-guidetree-iterations
  • --max-hmm-iterations
  • --maxnumseq
  • --maxseqlen
  • --outfmt
  • --output-order
  • --residuenumber
  • --resno
  • --seqtype
  • -t
  • --wrap

Additional arguments can be specified under the tool_args argument.


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