WRAPPER DEPRECATED – one can install mafft on Agave API and use this wrapper as a prototype –
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of about 200 sequences), FFT-NS-2 (fast; for alignment of about 10,000 sequences), etc. See http://mafft.cbrc.jp/alignment/software/. The manual is also available here: http://mafft.cbrc.jp/alignment/software/manual/manual.html
name of file to be evaluated on the Discovery Environment (DE), see details for supported input formats.
file.path
optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory
type
Two options "PROTEIN" or "DNA". This defines the type of sequences in the file, either proteins or nucleotides.
aln.filetype
Mafft does alignment of sequences, this option selects the file type of that result file. There are two options FASTA and CLUSTALW
args
Optional for arguments (i.e. flags). The Mafft model has much additional functionality that is not in this wrapper function (http://mafft.cbrc.jp/alignment/software/manual/manual.html#lbAI), see details. This option allows users to add anything that is not included (.i.e. args="–auto"), which automatically selects an appropriate strategy according to data size, see details.
out.name
the name to given to the output file (default mafft.aln)
job.name
the name to give the job being submitted
print.curl
Prints the curl statement that can be used in the terminal, if curl is installed on your computer
shared.username
With iPlant you have the ability to share folders with other users. If someone has shared a folder with you and you want to run a job with them, enter their username for this input.
suppress.Warnings
This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.