tools: add 3dtrees metadata wrapper - #2

Closed

kgerb wants to merge 38 commits into

3dtrees_metadata_v1_0_0

Commits on Mar 30, 2026

Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1
planemo-autoupdate
committed
121700e

Commits on Apr 20, 2026

Fix GTF format in annotation file parameters
pavanvidem
authored
8783413
Change BAM format from uppercase to lowercase
pavanvidem
authored
c0f9f3e
set annotation type to tar
pavanvidem
authored
1c63bc5

Commits on Apr 21, 2026

Fix typo in annotation_path parameter attribute
pavanvidem
authored
140b64d
Rename annotation_path.tgz to annotation_path.tar
pavanvidem
authored
af6fedf
Fix annotation path in ribotaper_part3_main.xml
pavanvidem
authored
5f68944
Rename annotation_path.tar to annotation_path.tgz
pavanvidem
authored
62c72d9
revert ftype to tgz
pavanvidem
authored
75d41eb
revert annotation path file extension
pavanvidem
authored
495616b

Commits on Apr 23, 2026

Update tar command for handling tgz files
pavanvidem
authored
20ae929

Commits on Apr 24, 2026

Change annotation path format from tgz to tar.gz
pavanvidem
authored
2ca3c27
add &&
pavanvidem
authored
706d988
add another test to see if it runs tar -xvf instead of tar - xvzf
pavanvidem
authored
5af16ee

Commits on Apr 28, 2026

Fix `no_interp` parameter in Cellpose-SAM wrapper
kostrykin
authored
0112c53
Fix `remote_repository_url`
kostrykin
authored
d39c477

Commits on Apr 30, 2026

Commits on May 4, 2026

Merge pull request #1825 from planemo-autoupdate/tools/rna_tools/ribotaper
pavanvidem
authored
496a77a
Updating tools/llm_hub from version 2.32.0 to 2.33.0 (#1856)

gxydevbot
and
planemo-autoupdate
authored
e160e1c
Apply suggestion from @pavanvidem
pavanvidem
authored
820df14
Update tools/cellpose_v4/.shed.yml
kostrykin
authored
18f46de

Commits on May 6, 2026

Fix RAG Retriever crash on markdown files (#1859)
arash77
authored
52a7de6

Commits on May 7, 2026

Use snapshot_download instead of SentenceTransformer.save() in download_embeddings.py (#1858)
arash77
authored
b095395

Commits on May 8, 2026

Updating tools/rna_tools/sortmerna from version 4.4.0 to 5.0.0 (#1857)

gxydevbot
and
planemo-autoupdate
authored
cc25c4d
add WebAtlas pipeline 0.5.3 (#1794)
dannyspadaro
authored
a777314

Commits on May 10, 2026

Fix Tiara wrapper when outputs are missing (#1846)
Minamehr
authored
990b334

Commits on May 12, 2026

Updating tools/llm_hub from version 2.33.0 to 2.36.0 (#1861)

gxydevbot
and
planemo-autoupdate
authored
018284a
Logan Proteins minor fix (#1860)
SaimMomin12
authored
68a35aa
Update mafft.xml (#1863)

SirKekstington
and
bgruening
authored
3167561
Merge pull request #1853 from kostrykin/kostrykin-patch-2
pavanvidem
authored
9bfce35

Commits on May 13, 2026

updated opsin and added shed.yml file (#1866)

hechth
and
bgruening
authored
431176b

Commits on May 16, 2026