[EMBOSS] Add Needleall tool (v6) and bump version for needle to v6

[shiltemann]

Added the needleall tool to the emboss suite. This tool is new in version 6. Since the needle tool is extremely similar I bumped its version as well and added some additional parameters.

I hope to be able to upgrade some of the other tools as well in the future. For reference, these are the most popular emboss tools on EU (thanks @bgruening!), so we can prioritize these for a version bump.

primersearch81/5.0.0.1 | 139259
geecee41/5.0.0 | 49077
needle56/5.0.0.1 | 8152
textsearch98/5.0.0 | 6872
revseq82/5.0.0 | 4728
sixpack90/5.0.0.1 | 4684
transeq101/5.0.0 | 4677
fuzznuc37/5.0.3 | 4372
extractseq35/5.0.0 | 2734
water107/5.0.0.1 | 2335
getorf42/5.0.0.1 | 2004
infoseq46/5.0.0 | 1453
pasteseq66/5.0.0.1 | 1322
tranalign100/5.0.0 | 1196
seqret84/5.0.0 | 886
matcher52/5.0.0.1 | 787
skipseq91/5.0.0.1 | 754
wordmatch110/5.0.0.1 | 687
palindrome65/5.0.0.1 | 530
cpgplot15/5.0.0 | 524
cusp17/5.0.0 | 507
fuzzpro38/5.0.0 | 505

ping also @bernt-matthias since we chatted about this

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[bernt-matthias]

Thanks fro starting this.

Wondering if we should try to bump all the tools that have tests? But might be to much work. Up to you.

[shiltemann]

Thanks for the review @bernt-matthias 👍 I was thinking of opening another PR where I bump the version of all tools and work -hopefully collaboratively- on updating the other tools there. But I would like to get needleall in a bit sooner if possible, so doing that first.

[bgruening]

Another thing that makes it more complicated is that those tools are not a Suite. Once we push we change all tools.

Should we break tool linage here and fix also the tool IDs?

[shiltemann]

@bgruening sure, I can do that

[bernt-matthias]

Should we break tool linage here and fix also the tool IDs?

Then we would have 2 of each tool (or at least those where we would change the ID) in the tool panel. Would not like this.

[bgruening]

Yes I also don't like it :(
But, its unlikely that we update all tools in one go, thus creating many new versions for the tools many without changes.
It would give us a clean base, we can create a proper suite of tools so people have the choice of what to install, and finally fix the tool-IDs which are very annoying e.g. in TPV.

Admins need to install those (new) tools manually either way and with that, they could "hide" the old versions.

On the other hand, workflows will not be as easy to update.

@galaxyproject/iuc any opinions.

[bgruening]

xref: https://help.galaxyproject.org/t/tcode-and-other-emboss-programs/13368

[shiltemann]

@bgruening ok I restructured this as a new tool suite. (Not sure why the tests are suddenly failing, they pass locally and passed before moving to their own folder, will look into it next week)

[bgruening]

This looks good to me. Happy to merge. @bernt-matthias is this ok for you as well?

[bgruening]

Thanks!

[bernt-matthias]

Ping @nsoranzo ?

[nsoranzo]

You should be able to easily move tools/emboss_5/emboss_backtranseq.xml to the new suite as it already uses emboss 6.6.0 .

[shiltemann]

@nsoranzo thanks, good to know, I will put that at the top of my list of next tools to add to the suite 👍