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[Community Tool Table Generation] Update the process to curate TS filtered community tool table #5503

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Nov 6, 2024
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[Community Tool Table Generation] Update the process to curate TS filtered community tool table #5503

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44 changes: 17 additions & 27 deletions topics/dev/tutorials/community-tool-table/tutorial.md
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Expand Up @@ -100,55 +100,45 @@ Once you have a list of the ToolShed categories that you wish to keep, you can s

The Pull Request will be reviewed. Make sure to respond to any feedback.

Once the Pull Request is merged, the interactive table will be created and made available online at `https://galaxyproject.github.io/galaxy_codex/<your community>`.
Once the Pull Request is merged, a table with all tool suites and a short description will be created in `communities/<your community>/resources/tools_filtered_by_ts_categories.tsv`

# Review the generated interactive table
# Review the generated table to curate tools

The interactive table will contain all the tools associated with the ToolShed categories that you selected. However, not all of these tools might be interesting for your community.
The generated table will contain all the tools associated with the ToolShed categories that you selected. However, not all of these tools might be interesting for your community.

Galaxy Codex allows for an additional optional filter for tools, that can be defined by the community curator (maybe that is you !).
Galaxy Codex allows for an additional optional filter for tools, that can be defined by the community curator (maybe that is you!).

The additional filter must be stored in a file called `tools_status.tsv` located in `data/community/<your community>`. The file must include 3 columns (without header):
1. The `Galaxy wrapper id` corresponding to the IDs in the `tools.tsv` file in `results/<your community>`.
2. Whether the tool should be included in the final table (TRUE/FALSE).
3. Whether the tool is deprecated (TRUE/FALSE).
The additional filter must be stored in a file called `tools_status.tsv` located in `communities/<your community>/metadata`. The file must include at least 3 columns (with a header):
1. `Suite ID`
2. `To keep` indicating whether the tool should be included in the final table (TRUE/FALSE).
3. `Deprecated` indicating whether the tool is deprecated (TRUE/FALSE).

Example of the `tools_status.tsv` file:
```
To keep Deprecated
abacas TRUE FALSE
abricate TRUE FALSE
abritamr TRUE FALSE
```

Have a look on the [microGalaxy tool stats TSV](https://github.com/galaxyproject/galaxy_codex/blob/main/data/communities/microgalaxy/tool_status.tsv) for
an example of the file that is used to manually filter the tools for a community.

## Add a tools status list
To generate this file, we recommend you to use the `tools_filtered_by_ts_categories.tsv` file.

> <hands-on-title>Review tools in your community table</hands-on-title>
>
> 1. Download the `tools.tsv` file in `results/<your community>`.
> 2. Open `tools.tsv` with a Spreadsheet Software.
> 1. Download the `tools_filtered_by_ts_categories.tsv` file in `communities/<your community>/resources/`.
> 2. Open `tools.tsv` with a Spreadsheet Software
> 3. Review each line corresponding to a tool
>
> You can also just review some tools. Those tools that are not reviewed will be have `FALSE` in the `Reviewed` columns the updated table.
>
> 1. Change the value in the `Reviewed` column from `FALSE` to `TRUE` (this will be done automatically if an entry of the tool in `tools_status.tsv` exists).
> 2. Add `TRUE` to the `To keep` column if the tool should be kept, and `FALSE` if not.
> 3. Add `TRUE` or `FALSE` also to the `Deprecated` column.
>
> 4. Copy paste the `Galaxy wrapper id`, `To keep`, `Deprecated` column in a new table (in that order).
> 1. Add `TRUE` to the `To keep` column if the tool should be kept, and `FALSE` if not.
> 2. Add `TRUE` or `FALSE` also to the `Deprecated` column.
>
> This can also be done using the reference function of your Spreadsheet Software.
>
> 5. Export the new table as TSV (without header).
> 6. Submit the TSV as `tools_status.tsv` in your community folder.
> 5. Export the new table as TSV
> 6. Submit the TSV as `tools_status.tsv` in your `communities/<your community>/metadata/` folder.
> 7. Wait for the Pull Request to be merged
>
{: .hands_on}

You should have now an interactive table reflecting the Galaxy tool landscape for your community. You can step-by-step review all tools in your community and update the `tools_status.tsv` file. You could also share this file with your community members and discuss weather the tool should be kept or not. Collaborative work could be established using google spreadsheet.

Once merged, a `curated_tools.tsv` file will be generated in `communities/<your community>/resources/` folder reflecting the Galaxy tool landscape for your community. You can step-by-step review all tools in your community and update the `tools_status.tsv` file. You could also share this file with your community members and discuss weather the tool should be kept or not. Collaborative work could be established using google spreadsheet.

# Embed the interactive table in your community page on the Hub

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