[WIP] ProteoRE ID_converter tool

[combesf]

Proteore id_converter tool
version 20210601
for review, thank you

[combesf]

I still have an error in the tool test here.
The error is :
parameter 'mapping_file': requires a value, but no legal values defined

But in the xml file, in the test lines, mapping_file is affected, so I don't understand ...

If someone could help here please ???
thansk a lot
@bgruening @vloux

[bgruening]

we should stick to small letters for variable names

[bgruening]

this here needs to be a value from your loc file.

https://github.com/galaxyproteomics/tools-galaxyp/pull/602/files#diff-1fcdfc7eef4418ad2c2fb5d674d84ecc7d287a211349e35843d9a6e5a1d6fcbe

So in this case the value= should be human_id_mapping

[bgruening]

@combesf can you have a look at this tool: https://github.com/bgruening/galaxytools/tree/master/tools/general_mapping

Its more generic I think and maybe you can use that tool instead?

[yvandenb]

can you have a look at this tool: https://github.com/bgruening/galaxytools/tree/master/tools/general_mapping
@bgruening : not sure that these tools are exactly the same; btw I was unable to find it in the TS so that we can install it on our dev-instance for evaluation purpose, could provide us with the exact name or a link ? is this tool deployed in usegalaxy.eu ?

[foellmelanie]

Hi @yvandenb I am not sure where the general mapping tool is but I think the 'uniprot_rest_interface' Uniprot tool can do the ID conversions for many different IDs and organisms: https://toolshed.g2.bx.psu.edu/repository?repository_id=c8774310981b07c5 It's also installed on the EU server.

[bgruening]

@combesf, @yvandenb I never published the tool in the toolshed, but at this time I wanted to solve the exact same problem as you, but in a more general way: https://github.com/bgruening/galaxytools/blob/master/tools/general_mapping/readme.md

In essence, an admin can create config files, of arbitrary mapping files. One tool that can map IDs for proteomics and physics and so on...