rPlant (version 1.2)

RunParsdna: Run Phylip Parsimony

Description

This function will submit a parsimony analysis job to Phylip on iPlant's DE

Usage

RunParsdna(user.name, token, DE.file.name="", DE.file.path="", job.name=NULL)

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

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 for submitting Phylip jobs with nucleotide data for a parsimony analysis.

See Also

SubmitJob

Examples

# RunParsdna(user.name, token, DE.file.name="ex.lp.fasta", DE.file.path="", job.name="PhylipParsimony1")