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galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
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shed-tools options -y and -t are confusing #72

Open Petraea opened 6 years ago

Petraea commented 6 years ago

Hi there, I just had a devil of a time getting shed-tools to work because of confusion between passing in a yml tool file (-t) and passing in a yml tool string (-y). Is there some way to clarify this further in the documentation?

Petraea commented 6 years ago

A comment from the Oslo 2018 Elixir training course. :)

rhpvorderman commented 6 years ago

Sure. Can you exactly state how you were confused?

Edit: Pull requests are also welcome ;-). You can find the information in the _parser() method on line 268 of ephemeris/shed_tools.py

drosofff commented 6 years ago

-f instead of -t ?

I have to admit that -t is a bit counter intuitive for a file, plus it reminds the -t option of planemo commands which stands for toolshed targets

rhpvorderman commented 6 years ago

I fail to see how -t for tools file can be extremely confusing. But I indeed see how the -y for the yaml string can be confusing if there also is a yaml tool file. Maybe we should include an example in the usage for the -y flag?

drosofff commented 6 years ago

I didn't say it's confusing ;-) But IMHO in tools file the most important word is file, especially in the perspective of running a command line.

rhpvorderman commented 6 years ago

I agree, but everyone who has used this tool before now does expect a -t flag. And I feel bad about breaking their assumptions ;-).

drosofff commented 6 years ago

I understand quite well ! I would be among the impacted users ;-) What about -t OR -f mapping to the same arg ? Not sure it is in the best practices list tough

rhpvorderman commented 6 years ago

Since we already broke everyone's script with release 0.8 I see no objection in doing this again. But I propose then that we use the same flags for all ephemeris tools. Now run-data-managers uses --config for its file, for example. Let's unify this so ephemeris becomes more coherent. Are there some UNIX conventions that we can use? Hate to reinvent the wheel here ;-).