diff --git a/README.md b/README.md index 53cc71a1..cb842f9e 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,16 @@ Galaxy Tool Metadata Extractor # What is the tool doing? +![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 @@ -89,12 +93,3 @@ The script will generate a TSV file with each tool found in the list of GitHub r [--keep ] ``` -### 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` diff --git a/docs/images/Preprint_flowchart.drawio b/docs/images/Preprint_flowchart.drawio new file mode 100644 index 00000000..fb95c305 --- /dev/null +++ b/docs/images/Preprint_flowchart.drawio @@ -0,0 +1,146 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/images/Preprint_flowchart.png b/docs/images/Preprint_flowchart.png new file mode 100644 index 00000000..40829e66 Binary files /dev/null and b/docs/images/Preprint_flowchart.png differ diff --git a/docs/images/flowchart_figs/redo.png b/docs/images/flowchart_figs/redo.png new file mode 100644 index 00000000..478e116f Binary files /dev/null and b/docs/images/flowchart_figs/redo.png differ