rename .name to .element_identifier

[bernt-matthias]

for the remaining tools

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)

[bgruening]

Remove the r-linter ;)

[bernt-matthias]

Remove the r-linter ;)

We have to restist this impulse :) linters are less annoying than ugly inconsistent code.

[lecorguille]

Hey, ipo was integreted before the arrival of the r-linter 😇

[lecorguille]

If I merge now, do you know if the "Check file sizes" will be an issue for the publishing in the TS?

[bernt-matthias]

If I merge now, do you know if the "Check file sizes" will be an issue for the publishing in the TS?

Deployment is done independent of the "Check file sizes test": https://github.com/workflow4metabolomics/tools-metabolomics/blob/7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca/.github/workflows/pr.yaml#L221C56-L221C56

At IUC we also deploy now also in case of tool linter warnings (but they are still shown in the PRs).

I just reopened because I had the impression that tool tests failed.

[bgruening]

Ship it? Or not?

[bernt-matthias]

Seems that this was not deployed: https://github.com/workflow4metabolomics/tools-metabolomics/actions/runs/6115157809

ipo4xcmsSet fails with

Error in ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass) : 
  object 'peakpicking_best_params' not found
Execution halted

There is also a warning, but likely unrelated

rror in plot.new() : could not open file '../IPO_results/rsm_1.jpg'
In addition: Warning message:
In dir.create(subdir) :
  cannot create dir '../IPO_results', reason 'Read-only file system'
Error in plotting (see above), but IPO continues to work normally!

[bernt-matthias]

I opened three new PR. The first should fix the IPO bug. The other two just add a bugus change to trigger deployment.

Guess having independent PRs makes deployment easier.