From 26a2765531c66beda406afb12e0198a24b2b566e Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 24 Jan 2024 15:58:33 +0100 Subject: [PATCH] Update docs (#51) * update flowchart * add new flowchart figure and use in readme * readme * update readme (#48) * Update docs (#50) * update readme * update readme --- README.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/README.md b/README.md index cb842f9e..cc8e9bdc 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,12 @@ Galaxy Tool Metadata Extractor ![plot](docs/images/Preprint_flowchart.png) + +This tool automatically collects a table of all available Galaxy tools including their metadata. The created table +can be filtered to only show the tools relevant for a specific community. **Learn [how to add your community](#add-your-community)**. + +The tools performs the following steps: + - Parse tool GitHub repository from [Planemo monitor listed](https://github.com/galaxyproject/planemo-monitor) - Check in each repo, their `.shed.yaml` file and filter for categories, such as metagenomics - Extract metadata from the `.shed.yaml` @@ -13,6 +19,10 @@ Galaxy Tool Metadata Extractor - Extract bio.tools information if available in the macros or xml - Check available on the 3 main galaxy instances (usegalaxy.eu, usegalaxy.org, usegalaxy.org.au) - Get usage statistics form usegalaxy.eu +- Creates an interactive table for all tools: [All tools](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/) +- Creates an interactive table for all registered communities, e.g. [microGalaxy](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/) + + # Usage @@ -93,3 +103,15 @@ The script will generate a TSV file with each tool found in the list of GitHub r [--keep ] ``` + + +## Add your community + +In order to add your community you need to: +- Fork this repository. +- Add a folder for your community in `data/communities`. +- Add at least the file `categories`. +- Add all `categories` that are relevant to initially filter the tools for your community. Possible categories are listed here [Galaxy toolshed](https://toolshed.g2.bx.psu.edu/). +- Make a pull request to add your community. +- The workflow will run every sunday, so on the next monday, your community table should be added to `results/` +