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regex find/replace: use format_source for output #679

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merged 2 commits into from
Feb 2, 2023

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jancrichter
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Version 1.0.2 of the tool uses format="input" in its output declaration. This creates an output with data type "input". I figure, the intention is instead to create an output with the same data type as the input. This should fix it, right?

Incidentally, this same error can currently be found in the Tool XML documentation.

Version 1.0.2 of the tool uses format="input" in its output declaration. This creates an output with data type "input". I figure, the intention is instead to create an output with the same data type as the input. This should fix it, right?

Incidentally, this same error can currently be found in the Tool XML documentation.
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Looks good to me!

@bernt-matthias good to go?

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format_source is more explicit (I remember that format="input" implies that the format is taken from the 1st input).

Can you add the ftype attribute to the in- and outputs in the tests.

@bernt-matthias bernt-matthias changed the title use format_source for output regex find/replace: use format_source for output Sep 28, 2022
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bernt-matthias commented Feb 1, 2023

Got it: in the last PR we set a profile. Problem is that format="input" was disabled for non legacy tools (ie tools which specify any profile): https://docs.galaxyproject.org/en/master/dev/schema.html#id1. This was unnoticed because the tests did not include ftype

Using format_source is the correct fix here.

bernt-matthias added a commit to bernt-matthias/galaxy that referenced this pull request Feb 1, 2023
@bernt-matthias bernt-matthias merged commit 3eaa2a2 into galaxyproteomics:master Feb 2, 2023
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this pull request Mar 7, 2023
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this pull request Jul 30, 2023
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3 participants