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Unused tool parameters #4085

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35 of 59 tasks
bernt-matthias opened this issue Oct 18, 2021 · 0 comments
Open
35 of 59 tasks

Unused tool parameters #4085

bernt-matthias opened this issue Oct 18, 2021 · 0 comments
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@bernt-matthias
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bernt-matthias commented Oct 18, 2021 •
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With galaxyproject/galaxy@fc264b1 the linter warns about parameters that are not used in the command (and configfiles, and other places). For debugging I verified almost all of them manually. I think many of them may qualify as paper cut.

In particular non_commercial_use:

  • add validator not allowing false
  • add exit 1 if not checked (otherwise linter would still complain)

So here is the list:

Done:

For my own reference: This is how the list was generated:

planemo ci_find_repos --exclude packages --exclude deprecated > repos.txt

while read line
do
echo $line; planemo lint --no_xsd -r -s output,tests,help,general,command,xml_order,citations,stdio $line
done < repos.txt > tests

grep "not found in command or configfiles" tests -B 2 | grep -v "Applying linter" | sed 's/.. WARNING: Param input \[/    - /; s/\].*//; s@Linting tool /home/berntm/projects/tools-iuc/@- [ ] @;' | grep -v '\-\-' | egrep -v "WARNING|ERROR"
@bernt-matthias bernt-matthias mentioned this issue Oct 18, 2021
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This was referenced Nov 25, 2021
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bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Aug 22, 2022
@bernt-matthias
add missing options to CLI
0b61b30 
see galaxyproject#4085
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Jan 10, 2023
@bernt-matthias
add missing options to CLI
ece0a99 
see galaxyproject#4085
bgruening pushed a commit that referenced this issue Jan 10, 2023
@bernt-matthias
hiccorrectmatrix: is writing to input file (#4670)
fa140a9 
* hiccorrectmatrix: is wrinting to input file

so we need to copy it

* skip from_workdir

* fix URLs

* workaround for a bug regarding parallel processing

that will be fixed in 3.7

* add missing options to CLI

see #4085

* more fixes:

- redundant name and argument
- 1 wrong parameter name in test
- 1 wrong option value and one missing option text

* fix duplicated output labels
pimarin pushed a commit to pimarin/tools-iuc that referenced this issue Feb 7, 2023
@bernt-matthias @pimarin
hiccorrectmatrix: is writing to input file (galaxyproject#4670)
486b379 
* hiccorrectmatrix: is wrinting to input file

so we need to copy it

* skip from_workdir

* fix URLs

* workaround for a bug regarding parallel processing

that will be fixed in 3.7

* add missing options to CLI

see galaxyproject#4085

* more fixes:

- redundant name and argument
- 1 wrong parameter name in test
- 1 wrong option value and one missing option text

* fix duplicated output labels
@bernt-matthias bernt-matthias mentioned this issue Nov 23, 2023
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@bernt-matthias bernt-matthias mentioned this issue Jan 19, 2024
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