Use BioBlend to get information on the tool json structure

[19ngxuan]

[19ngxuan]

Tools to read the tool shed. And figure out the parameters of the individual processing steps. This information might be useful for generating the implementation/ getting the tool steps.

[rmassei]

The API interacting with the Galaxy Toolshed (BioBlend) can help to get information about the tool's JSON structure and provide more information to the LLM about how the tool looks like.

Here the documentation:
https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html

Another point is that it would be beneficial to screen the tools in the 'Imaging' section, and the script should cross-check if the name of the tool exists or if it is making it up.
Other toughts @bernt-matthias?

Please @19ngxuan let me know if you need an example

[rmassei]

from bioblend import toolshed
import json

ts = toolshed.ToolShedInstance(url='https://toolshed.g2.bx.psu.edu')

rl = ts.repositories.get_repositories()

tools = ts.tools.search_tools('imgteam')

[bernt-matthias]

Other toughts

Do imaging tools have annotations like edam topics / operations or other xrefs that could be used to find the correct tool.

Datatypes of inputs or outputs files could be useful for filtering suitable tools? Or is it just always images?

[rmassei]

Script to get more information from BioBlend:
usegalaxy-eu/usegalaxy-eu-tools#838

[19ngxuan]

• line 123 for version
• line 148 search algo for tools
  https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/838/files

[19ngxuan]

maybe shortcut:

https://github.com/usegalaxy-eu/usegalaxy-eu-tools

• get the installed tools from here
• but still need tool versions from repository pr 838