new tool: galaxy wrappers for the pcdl physicell data lader command line commands #7034
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@elmbeech thanks! I added a few comments that apply for all tools. I think a macro file and a proper formatting will help a lot for further reivew.
Please have a look at the Galaxy Language Server, it has some build-in tools for auto-formatting.
| <requirement type="package" version="3.3.7">pcdl</requirement> | ||
| </requirements> | ||
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| <stdio> <exit_code range=":" level="log" description="hello world!"/> </stdio> |
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hello world is not a good description :)
But I guess this entire line can be removed
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hi @bgruening ,
thank you for reviewing!
unfortunately, this line cannot be removed.
if you write a python package with command line hocks, the python output is piped to sterr.
if i remove this line, galaxy thinks it always caught an error when the script runs successfully.
this is why i have to catch all exit_codes as log.
i agree, hello world! is not a good description.
i will change this to catch python script output.
would this be acceptable?
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I think what you are looking for is https://docs.galaxyproject.org/en/latest/dev/schema.html#error-detection e.g. detect_errors="exit_code" on the command tag. See other Python based tools here in IUC.
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No, exactly not.
As you can see, if I do so an error is detected, even if there is none.
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Ok, that mean that your tool is reporting an error code of 1, is that the case?
For any other tool, text on stderr is not a problem, you can instruct Galaxy to only react on error codes, not text on stderr.
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no it is not reporting an error code of 1.
as you can see, in this particular command (which in the pcdl command line version just output to the screen) , the bash line is catching the standard error with 2> and is writing this to version.txt.
and galaxy interpret this as error code 1.
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i followed this instruction in the galaxy documentation:
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I think this is what you mean with "langauage server". Could you please point me to what you mean with "macro"? |
Sure. https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements |
i think you mean: ``` type="boolean" truevalue="" falsevalue="--microenv false" checked="true" ``` Co-authored-by: Björn Grüning <[email protected]>
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