Hi,
I am developing a tool simillar to the MothurGUI-tool…
My question:
For some parameters like Boolean or Numbers there is a third option, called ‘none’.
save=F|F|none
What is this parameter used for?
Regards,
TL
That field is part of all the parameters. It is the outputType. It is used to indicate to the GUI what type of file this parameter will create when the command is run. In your example the save parameter does not create an output file so its output type is none. Let’s look at another example, the unique.seqs command:
commandName=unique.seqs
commandCategory=Sequence Processing
help=The unique.seqs command reads a fastafile and creates a name or count file.It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. If the sequence is unique the second column will just contain its name. The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.The unique.seqs command should be in the following format: unique.seqs(fasta=yourFastaFile)
citation=http://www.mothur.org/wiki/Unique.seqs
description=creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents
outputTypesNames=3
count=[filename],count_table-[filename],[tag],count_table
fasta=[filename],unique,[extension]
name=[filename],names-[filename],[tag],names
Boolean=0
Multiple=0
Numbers=0
String=0
inputGroupNames=1
namecount=count-name
inputTypes=count-fasta-name
count=F|T|namecount|none|none|count
fasta=T|T|none|none|none|fasta-name
name=F|T|namecount|none|none|name
You can see there are 3 outputTypes: fasta, name and count. The count parameter has an outputType of count, indicating that if a count file is provided to the command a count file will be created. The fasta parameter has output types of fasta and name, indicating that if a fasta parameter is provided the command will create a fasta and names file. The name parameter has an outputType of name, indicating that if a name file is provided then the command will create a new names file. The GUI uses the output types and their formats to “predict” mothur’s output filenames and autofill boxes in the GUI.
Hi westcott,
Thanks for your detailed informations.
Can I assume, that for Boolean/Multiple/String/Number there are never output files?
Regards,
TL
Yes, that’s how we have it set up now.