galaxyproject / galaxyproject/tools-iuc
Tool request: SpaMO
- Dominant language
- HTML
- Stars
- 201
- Forks
- 525
- Avg merge
- 23h 54m
- Merged PRs (30d)
- 59
Description
There is a tool from the MEME suite collection called [SpaMO](https://meme-suite.org/meme/doc/spamo.html) that might be quite useful for secondary motif detections.
The tool is also integrated in MEME-ChIP, which exist in Galaxy already, yet the tool is deactivated (see call below)
```
meme-chip /data/dnb06/galaxy_db/files/a/d/5/dataset_ad5775f4-26b7-42e8-a63f-e8256dd82418.dat -noecho -dna -o /data/jwd/main/047/350/47350655/working/dataset_16bb4fdf-ff9f-46d3-853a-6a21246076f8_files -order 1 -ccut 100 -group-thresh 0.05 -group-weak 0.0 -filter-thresh 0.05 -meme-mod zoops -meme-minw 5 -meme-maxw 20 -meme-nmotifs 5 -dreme-e 0.05 -dreme-m 5 -spamo-skip -fimo-skip
```
I think it would be quite useful if there is an options in the MEME-ChIP wrapper for SpaMO, or to integrate SpaMO in Galaxy.
Contributor guide
Research direction
Start by locating the existing MEME-ChIP Galaxy wrapper and the command shown in the issue, especially the `-spamo-skip` option. Determine whether SpaMO should be exposed through that wrapper or integrated separately; done when the chosen approach supports SpaMO in Galaxy and its behavior is covered by the project’s validation checks.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100