Fix mOTUs wrapper

[Minamehr]

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• 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)

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This PR updates the mOTUs profiler wrapper.
The mOTUs database is large, so only the existing lightweight wrapper test is kept in the tool XML, but Tested single-end, paired-end, and paired-end collection inputs locally.

[mvdbeek]

The SameStr mOTUs data manager (iuc/data_manager_samestr) has the same motus_db_versioned.path assumption this PR is fixing for the profiler — and it trips over it. Its mOTUs branch hard-codes:

#set $db_path = $db_source.motus_db.fields.path
#set $markers_info1 = $db_path + '/db_mOTU/db_mOTU_taxonomy_ref-mOTUs.tsv'
...
cp '$db_path'/db_mOTU/db_mOTU_versions ...

i.e. it assumes path is the parent of db_mOTU. But the mOTUs DM's value_translation (${GALAXY_DATA_MANAGER_DATA_PATH}/motus_database/${value}/db_mOTU) and this PR's new .loc.sample (path = /data/motus/db_mOTU) make path the db_mOTU folder itself — so SameStr's $path/db_mOTU/... doubles and fails (cp: can't stat .../db_mOTU/db_mOTU_versions: No such file).

We hit this building an mOTUs-derived SameStr DB as a reference-data bundle for idc. It works on usegalaxy.eu only because that particular install happens to have path = the parent (a db_mOTU/ subdir), which isn't universal.

Two questions:

1. Is path = the db_mOTU folder the intended canonical convention going forward (per the new .loc.sample + the value_translation)?
2. Would you be open to SameStr adopting the same robust probe you added here —

   if [ -d "$db_path/db_mOTU" ]; then db_path="$db_path/db_mOTU"; fi
   

   then reading the markers from $db_path directly — so both consumers agree regardless of which convention an install uses?

If that's the direction, we're happy to send the SameStr PR mirroring this. cc @SaimMomin12 (SameStr DM author + reviewer here) @Minamehr @bernt-matthias

[SaimMomin12]

@Minamehr Can you please check with this?

[mvdbeek]

Friendly ping on this — @Minamehr @SaimMomin12: any thoughts on whether path = the db_mOTU folder is the intended canonical convention (per this PR's .loc.sample + the DM value_translation)?

To make the concrete proposal easy to look at, I opened the analogous SameStr fix as a draft: galaxyproject/tools-iuc#8346 — it uses the exact same if [ -d "$path/db_mOTU" ] probe you added here, so both consumers agree regardless of which convention an install uses. Happy to adjust it to whatever convention you settle on.

[bernt-matthias]

Having db_mOTU/ subdir seems not necessary, but changing this might break existing installations? Maybe better change the dir at eu?

[mvdbeek]

That would be the cleaner fix, but is this not breaking any tools ? Has mOTUs never worked against a reference created by the data manager ?

[bernt-matthias]

If the tool never worked with the db_mOTU/ in the path we can and should remove it. But I do not know this.

@Minamehr ?