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Wrapper plugin question

I'm trying out the wrapper plugin development plugin and I have a few questions:

The output of the command line tool is a gff file which should be imported as annotations on the input sequence.  Is this possible?

Is there a way to see the actual command line that is being executed?  This would be very useful for debugging.

The tool I'm running requires the input file name be the last parameter on the command line.  Are the user selectable parameters placed after the command line that is configured in the previous window?

Thanks!

Mike

Michael Thon

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Unfortunately, annotation importers (such as gff) prompt the user for the sequence to attach the annotations to, so they don't work well under wrapper plugins.

But as it turns out, I was developing a new wrapper plugin the day before you asked this, where I wanted to do exactly that. So I extended our wrapper plugin system to support annotation generators. Unfortunately, the changes won't be available until Geneious 8.1, early next year.

In the meantime, if the command line program has an option to include the sequence data in the gff file (since the gff format optionally allows it to contain sequence data) then you should be able to get it working if you write it as a general wrapper plugin. If not, then the best you'll be able to do is to have it prompting the user to choose the file or document in Geneious that contains the sequence data each time they the plugin finishes.

And no, there isn't a way to see the actual command line. I'll probably include an option to allow that in future versions.

The user selectable options are replace by the [otherOptions] section in the command line template which by default looks like this

-in [inputFileNames] -out output [otherOptions]

If you want the input file name after the other options you could change it to something like this

-out output [otherOptions] -in [inputFileNames]

Hilary Miller 0 votes
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Thanks for the info.  I got the wrapper plugin working.  This is a new version of the Augustus plugin developed with the wrapper plugin instead of from scratch.  It seems to work fine now except that at the end of the analysis it asks the user for the sequence to import the features to.  That should be fixed with your next update.  

Michael Thon 0 votes
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