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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Query_tabular command line usage #5280

Open esraaelmligy opened 1 year ago

esraaelmligy commented 1 year ago

Hello, I am running the Galaxy Proteogenomics workflow through my command line and i seem to be stuck at how to execute the query_tabular tool in command line, can you please share with me a simplified method on how to imitate that step through my command line??

bgruening commented 1 year ago

It is using this python script under the hood: https://github.com/galaxyproject/tools-iuc/blob/0460711184f579a316f4393e4cd0663886295d48/tools/query_tabular/query_tabular.py

Does this help you?

esraaelmligy commented 1 year ago

Thank you so much for replying, yes this is actually the command line script i am trying to execute but i can't figure out the right way to do so

bgruening commented 1 year ago

You see here an example: https://github.com/galaxyproject/tools-iuc/blob/0460711184f579a316f4393e4cd0663886295d48/tools/query_tabular/filter_tabular.xml#L9

bernt-matthias commented 1 year ago

I guess this simplest and least error prone way to call Galaxy tools from the command line is to use the API (e.g. via bioblend).

If you really want to use it from the command line I guess we need more details of the problems that you have.