Update signalp to 4.1

[abretaud]

Hi,
As one of our users had problems with the signalp3.0 output, I had to update it to version 4.1.
Here's the modified xml and py
The doc and tests would need to be updated too, but I don't really have the time right now... I thought you could be interested anyway
Cheers

[peterjc]

Thanks Anthony, I'm not planning to work on this right away, but having the pull request here is useful.

I'd prefer to have the SignalP 3 and 4 wrappers as two separate tools, and related to that was wondering about splitting this suite of tools which are currently a single Tool Shed entry into their own independent Tool Shed entries. To that end, starting SignalP 4 as a new folder of its own makes sense.

I've deliberately not worked on this because SignalP (and TMHMM etc) are not open source so I cannot setup automated testing. This means any work on the tools becomes much more work due to manual setups for testing being essential. Sigh.

I even contacted the tool authors to ask about this - for example permission to redistribute the software for testing, but this was denied.

Also, what was going wrong with SignalP 3? We're still using that locally and recently ran into #24 following some changes to our cluster and how we run jobs.

[abretaud]

I've deliberately not worked on this because SignalP (and TMHMM etc) are not open source so I cannot setup automated testing. This means any work on the tools becomes much more work due to manual setups for testing being essential. Sigh.

Yes, that's also the reason I made this in a quick and dirty way

The problem I had with signalp3 was this error which was thrown with some of our test data. It's hard to investigate without the sources, and as 4.1 doesn't have this problem, I just updated and people are happy now :)

[peterjc]

Right - SignalP v3 seems to be two binary tools with a perl wrapper which doesn't check the two tools return the same number of results. Sometimes one seems to skip a sequence, leaving the output file messed up. I don't think I ever reduced this to a clear test case, but that assert was to guard against this.

[peterjc]

Note to self, the RXLR wrapper expects the old columns (using Python counting, 0 = ID, 18 = HMM_Sprob_score and 5 = NN_Ymax_pos), and would also need updating if used with this Signalp 4.1 wrapper.

[savipuray]

Hi,

Thanks for this Galaxy toolshed. It is really helpful for effector analysis.
I updated my toolshed to SignalP version 4.1, which is working perfectly. I was wondering if there was an updated RxLR wrapper that works for SignalP4.1. If not, I was wondering how to modify the existing wrapper for the purpose. Sorry if this is a dumb question. I am new to this and any help would be much appreciated.
Thank you!

Savithri

[peterjc]

The RXLR tool used the same version of SignalP as the tools cited, so in that sense it doesn't need changing.

If you want to apply the same ideas but with SignalP v4.1, then as per my earlier comment the parser needs updating as they changed the output. I have not sat down to do this:
#25 (comment)

I would strongly recommend you have both the old and the new SignalP installed, and use the old one with the RXLR tool.

[savipuray]

Thank you! That helps!