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CSV as Plugin Import

I'm trying to use the Wrapper Plugin Creator to make a plugin for a python program that runs through the command line. The program takes as input a CSV exported from a Geneious BLAST consensus results file. According to one of your help pages, the wrapper can accommodate a program which "Accepts input sequences as files on disk in a format that Geneious Prime can export." This would lead me to believe that CSV can be used as the input type, since Geneious can export such files. However, my only choices are .fasta.gz, .fasta, .fastq, .fastq.gz, .gb, .xml, .meg, .nex, .phy. I have the document type selected as "Multiple Alignment (4+ sequences)", but I did try selecting the other options, none of which seemed to have CSV available as a format. Similarly, I tried the different sequence type options to no avail. I have the plugin type selected as "General Operation", as its function is to take the CSV and parse the information in a particular way, creating a new output file sorted in a way that we need for further analysis. If you could advise as to how to select CSV as the input format, I would greatly appreciate it!

Chow

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Firstly, I apologize for the extremely slow reply! Somehow we overlooked this question until now.

Unfortunately you've run into a limitation in our code which detects which exporters are compatible with the type of documents the wrapper plugin accepts. We've fixed this for our next major release (2021.2) of Geneious Prime. Sorry, but I'm unable to think of a work-around for you in the meantime.

Please let us know if you have any further questions and we'll endeavor to answer more promptly next time!

Matt Kearse 0 votes
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Hi,

I saw the release notes for 2021.2 mentioning that this was fixed, so I excitedly updated to the beta (Geneious Prime® 2021.2.0, Build 2021-06-15 11:22).  It's still not allowing CSV as an input for wrapper plugins.  I tried creating a brand new plugin and going through all the Plugin Types, but none provided CSV as an option.  Is there a newer build?

Thank you!

Chow 0 votes
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Thanks for letting us know. It turns out this fix passed through our QA process successfully, but we made a mistake in our release process and this fix wasn't included in 2021.2.0 like it should have been. It will be in the next patch (2021.2.1) which will probably be available in about two weeks.

Sorry for the confusion and thanks again for pointing this out to us.

Matt Kearse 0 votes
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