galaxyproject / galaxyproject/ga2

support arbitrary number of additional assembly files

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Description

We would like to be able to list or display an arbitrary number of files for an assembly. Most assemblies will undergo post-analysis after being curated and uploaded to NCBI. We want to make these files available for listing or display, with the option to download them.

A few post analysis:
- pretext
- EGAPx
- RepeatModeler

## Pretext
if we take following assembly [bTaeGut2.hap1.W.cur.20220905.fasta.gz](https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut2/assembly_curated/bTaeGut2.hap1.W.cur.20220905.fasta.gz) found on the S3 bucket we have the following pretext files:
- [bTaeGut2.hap1.W.cur.20220905.pretext.gz](https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut2/assembly_curated/bTaeGut2.hap1.W.cur.20220905.pretext.gz)
- [bTaeGut2.hap1.W.cur.20220905.pretext.png.gz](https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut2/assembly_curated/bTaeGut2.hap1.W.cur.20220905.pretext.png.gz)

## Repeat Modeler
- [GCA_009769605.1.repeatModeler.families.fa.gz](https://hgdownload.soe.ucsc.edu/hubs/GCA/009/769/605/GCA_009769605.1/GCA_009769605.1.repeatModeler.families.fa.gz)
- [GCA_009769605.1.repeatModeler.2bit](https://hgdownload.soe.ucsc.edu/hubs/GCA/009/769/605/GCA_009769605.1/GCA_009769605.1.repeatModeler.2bit)

I suggest that with add the key additional_files to genomes section of our json files:

**organism.json**
```json
[
{
"assemblyCount": 1,
"assemblyTaxonomyIds": [
"10013"
],
"genomes": [
{
"accession": "GCA_031878675.1",
"annotationStatus": null,
"chromosomes": 40,
"coverage": "45.0x",
"gcPercent": 41,
"geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/031/878/675/GCA_031878675.1/genes/GCA_031878675.1_mThoBot2.hap1.augustus.gtf.gz",
"isRef": "No",
"length": 2025633870,
"level": "Chromosome",
"ncbiTaxonomyId": "10013",
"scaffoldCount": 629,
"scaffoldL50": 12,
"scaffoldN50": 64418693,
"species": "Thomomys bottae",
"speciesTaxonomyId": "10013",
"strain": null,
"ucscBrowserUrl": null
"addition_files": [],
}
],
"ncbiTaxonomyId": "10013",
"species": "Thomomys bottae"
},
]
```

**genomes.json**
```json
[
{
"accession": "GCA_003287225.2",
"annotationStatus": null,
"chromosomes": null,
"coverage": "57.3x",
"gcPercent": 39,
"geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/003/287/225/GCA_003287225.2/genes/GCA_003287225.2_phaCin_HiC.augustus.gtf.gz",
"isRef": "No",
"length": 3192623321,
"level": "Scaffold",
"ncbiTaxonomyId": "38626",
"scaffoldCount": 1245,
"scaffoldL50": 3,
"scaffoldN50": 428240489,
"species": "Phascolarctos cinereus",
"speciesTaxonomyId": "38626",
"strain": null,
"ucscBrowserUrl": null
"addition_files": [],
},
]
```
## Addition_files description
```json
{
"additional_files": [
{
"title": "Pretext files",
"files": [
{
"label": "Pretext image",
"url": "https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut2/assembly_curated/bTaeGut2.hap1.W.cur.20220905.pretext.png.gz",
},
{
"label": "Pretext file",
"url": "https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut2/assembly_curated/bTaeGut2.hap1.W.cur.20220905.pretext.gz",
}
],
}
]
}
```

### Implementation
Iterations:
1. For the initial implementation, I would like to list the files and make them available for download by users.
- title will be used as header for that section
- label could be used as name for the download link/button
2. In the next iteration, we aim to provide the ability to display different collections of files in various ways by introducing reusable components. For pretext files, we would like to display the associated PNG image directly on the page while making the pretext.gz file downloadable. To support this, we plan to implement a new component, tentatively named PretextData, which will accept both a png.gz file and a pretext.gz file as input.
Additionally, we will implement a ListFile component to display files in a simple list format with download options. More components can be developed as needed to support different file types and display requirements."

Here is a not see nice looking example, but it can be used as an example. We are displaying the png screen shot and making the pretext file downloadable
![Image](https://github.com/user-attachments/assets/1716ba71-a1f6-4265-94e4-cf71db8fa26c)

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