galaxyproject / galaxyproject/tools-iuc

Tool request: SpaMO

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tool request
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23h 54m
Merged PRs (30d)
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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

Open the contributing 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

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