Call for Support: Updating outdated metagenomics tools on IUC

Currently several metagenomics tool wrappers in tool-iuc are lagging behind their upstream versions. This means:

- End Users may be missing bug fixes, new features, or performance improvements available upstream.
- Tool behavior in Galaxy may no longer match the documented behavior of the underlying software, which can lead to reproducibility issues.
- Outdated wrappers signal to the community that a tool may be unmaintained, even when the science behind it is still very much in active use.
- The Galaxy Training Network tutorials does not reflect the latest state of the tool.

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**Request for assistance**

We would like to push this further and make it a _**coordinated, community-wide effort**_ to update the outdated metagenomics tool wrappers listed below so that they track their current upstream releases.

We request the involvement of microGalaxy SIG members in this effort, given the group's collective expertise in the metagenomics tool ecosystem on Galaxy. Specifically, we welcome contributions from:

- Tool authors and maintainers within the SIG who can confirm the current upstream release and any breaking changes
- SIG members with experience in Conda/Bioconda recipes, XML tool wrappers, and Planemo testing who can carry out or review the updates
- Anyone in the SIG willing to help coordinate, triage, or track progress on this effort

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**Tools that need updating (Sorted by tool usage on usegalaxy.eu)**

| Tool name | Current version in Galaxy | Latest upstream version | Existing PR | Status | Overall tool-usage |
| :----------- | ------------------------: | ----------------------: | :---------- | :----------- | -----------------: |
| prokka | 1.14.6 | 1.15.6 | #7542 | *open* | **1,346,464** |
| bakta | 1.9.4 | 1.12.1 | #6566 | *open* | **270,624** |
| metaphlan | 4.2.6 | 4.2.6 | #8199 | *merged* | **66,706** |
| freyja | 2.0.1 | 2.0.3 | #7539 | *merged* | **24,656** |
| mothur | 1.39.5 | 1.48.6 | - | *open* | **20,928** |
| megan | 6.21.7 | 6.25.10 | #5174 | *open* | **6,317** |
| mmseq2 | 17-b804f | 18-8cc5c | - | *open* | **6,037** |
| semibin | 2.1.0 | 2.4.1 | - | *open* | **4,872** |
| maaslin2 | 1.18.0 | 1.22.0 | - | *open* | **4,725** |
| recentrifuge | 1.16.1 | 2.1.2 | #7571 | *open* | **3,664** |
| kleborate | 2.3.2 | 3.2.4 | - | *open* | **3,187** |
| vegan | - | - | #3966 | *merged* | **3,165** |
| picrust2 | 2.5.3 | 2.6.3 | - | *open* | **3,046** |
| drep | 3.7.1 | 4.0.0 | - | *open* | **2,882** |
| instrain | 1.5.3 | 1.9.0 | #4307 | *open* | **434** |
| DISCO | 1.2 | 1.3 | - | *open* | **498** |
| amplican | 1.14.0 | 1.32.1 | #4305 | *open* | **376** |
| kmer2stats | 1.0.1 | 1.0.3 | #7952 | *merged* | **376** |
| decontam | 1.22.0 | 1.30.0 | #6634 | *open* | **101** |
| deacon | 0.12.0 | 0.16.0 | - | *open* | — |
| PhyloPhlAn | 3.1.1 | 3.1.1 | #7067 | needs review | — |
| straindesign | 3.2.2 | 3.2.3 | #5825 | *open* | — |

_This list might be incomplete, but please feel free to add/remove/adapt accordingly_

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**How to contribute**

We ask interested SIG members and other contributors to follow the process outlined below:

1. Comment on this issue indicating which tool(s) you intend to work on, in order to avoid duplication of effort.
2. Consult the tool's upstream repository to identify the current release version and review the associated release notes or changelog.
3. Update the Bioconda/Conda requirement version and the corresponding `` version attribute in the wrapper's XML.
4. Update or add test cases to cover any new or modified parameters, and confirm that planemo test passes locally.
5. Submit a pull request against IUC repo, referencing this issue and applying the microGalaxy label.

We would appreciate microGalaxy SIG members' participation in this effort, whether through direct contributions, review support, or coordination. Please indicate your interest in the comments below.

CC: @paulzierep @bebatut @bernt-matthias @Minamehr @RZ9082

Choose an unclaimed tool from the table, then consult its upstream repository and release notes. Update the corresponding XML wrapper version and Bioconda/Conda requirement, add or update tests for changed parameters, and run planemo test locally. Done means a passing update submitted as a pull request against the IUC repository referencing issue #8301.

Written by the indexing model from the issue text.