rPlant (version 1.2)

RunClustal: ClustalW alignment

Description

This function will submit a ClustalW job to iPlant's DE

Usage

RunClustal(user.name, token, DE.file.name="", DE.file.path="", job.name=NULL, version="ClustalW2-2.1")

Arguments

user.name

iPlant Discovery Environment user name

token

A validation tool used in place of unencrypted passwords

DE.file.name

Name of file to be evaluated on the Discovery Environment (DE)

DE.file.path

Optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory

job.name

The name to give the job being submitted

version

ClustalW version, options include ClustalW2-2.1, clustalw2-lonestar-2.1, clustalw-ranger-1.0

Value

• Text listing action as either being a "success" or "error". If an error, then a message stating the error should also be reported.

Details

The function is a wrapper function to submit ClustalW alignment jobs through the iPlant api.

See Also

SubmitJob

Examples

# RunClustal(user.name, token, DE.file.name="ex.lp.fasta", job.name="clustalw.Job1", DE.file.path="", version="ClustalW2-2.1")