From 50000d92e31da64acfad7f8769a2eb66d916971a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 6 Nov 2024 18:02:20 +0100 Subject: [PATCH] Update the process to curate TS filtered community tool table --- .../community-tool-table/tutorial.md | 44 +++++++------------ 1 file changed, 17 insertions(+), 27 deletions(-) diff --git a/topics/dev/tutorials/community-tool-table/tutorial.md b/topics/dev/tutorials/community-tool-table/tutorial.md index e9d189335e0071..7e708ec8c935e2 100644 --- a/topics/dev/tutorials/community-tool-table/tutorial.md +++ b/topics/dev/tutorials/community-tool-table/tutorial.md @@ -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/`. +Once the Pull Request is merged, a table with all tool suites and a short description will be created in `communities//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/`. The file must include 3 columns (without header): -1. The `Galaxy wrapper id` corresponding to the IDs in the `tools.tsv` file in `results/`. -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//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. > Review tools in your community table > -> 1. Download the `tools.tsv` file in `results/`. -> 2. Open `tools.tsv` with a Spreadsheet Software. +> 1. Download the `tools_filtered_by_ts_categories.tsv` file in `communities//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//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//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