Document how parameters in sections are referenced #11026
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Thanks @bernt-matthias for improving our tool documentation constantly, this is really appreciated!
lib/galaxy/tool_util/xsd/galaxy.xsd
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| Until profile 21.01 `parameter_name` was sufficient (https://github.com/galaxyproject/galaxy/pull/9493/files). | ||
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| Note that references to other parameters in the `<inputs>` section are only possible if the reference is in the same section or its parents, therefor only `parameter_name` is used. |
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Can you provide an example here?
In theory we could have a parameter foo in the top-level inputs and a parameter foo in a section. Do we?
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Can you provide an example here?
Yes.
In theory we could have a parameter foo in the top-level inputs and a parameter foo in a section. Do we?
Yes, but this is discouraged ... nevertheless it might occur in automatic tool building (e.g. in OpenMS I had the case, but luckily no cross reference was needed). Wondering if we should file an issue for this?
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Since this is the same for repeats and conditionals .. is there a way to have this docs also there? Also it would be good to link this to the docs of |
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
mvdbeek
changed the title
galaxyproject#11026 extended the description on how parameters in sections are referenced. this already included syntax that is not merged yet: galaxyproject#9493 this PR reverts this, see galaxyproject#9493 (comment)
Quite confusing for tool developers ...
Maybe parts of the text could be duplicated / moved to other parts of the docs.
Is it a bug that cross referring inputs is only possible on the same or parent levels? From inspecting the code it also appeared to me that the reference needs to be before the referring parameter (in the xml file). The reason for both is in this function
galaxy/lib/galaxy/tools/__init__.py
Line 1231 in 91580d1