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update readme #48

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15 changes: 4 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,13 @@ Galaxy Tool Metadata Extractor
![plot](docs/images/Preprint_flowchart.png)

- 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 metagenomics or other tag
- Check in each repo, their `.shed.yaml` file and filter for categories, such as metagenomics
- Extract metadata from the `.shed.yaml`
- Extract the requirements in the macros or xml to get version supported in Galaxy
- Check against conda the available version
- Check available against conda version
- 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

# Usage

Expand Down Expand Up @@ -91,12 +93,3 @@ The script will generate a TSV file with each tool found in the list of GitHub r
[--keep <Path to to-keep tool file category file>]
```

### Filter tools for microbial data analysis

For microGalaxy, a Bash script in `bin` can used by running the script

```
$ bash bin/extract_microgalaxy_tools.sh
```

It will take the files in the `data/microgalaxy` folder and export the tools into `microgalaxy_tools.csv`