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Fix test parameters that are not defined in the inputs #4095

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bernt-matthias opened this issue Oct 20, 2021 · 4 comments
Open
30 of 67 tasks

Fix test parameters that are not defined in the inputs #4095

bernt-matthias opened this issue Oct 20, 2021 · 4 comments
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@bernt-matthias
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bernt-matthias commented Oct 20, 2021 •
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There are many cases where test parameters are used that are not defined in the inputs.

I guess most cases are easy to solve, but may require a bit of research:

  • check if the parameter was there in the past and was removed, then we can also remove the test parameter
  • check the underlying tools if there is such a parameter and maybe add it to the inputs (ie. it was forgotten to be implemented in the tool)
  • ...

Here is the list of tools that currently suffer from this (please put your name / link to the PR next to the tool if you are working on this):
@bernt-matthias bernt-matthias mentioned this issue Nov 15, 2021
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bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Nov 22, 2021
@bernt-matthias
fix unused inputs
cb274f3 
kmerfilter: barcode_encoding in inputs but unused
populations: fastphase present in inputs but unused
shortreads: add_log used in test but absent from inputs

xref galaxyproject#4095
This was referenced Nov 22, 2021
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bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Nov 22, 2021
@bernt-matthias
add missing arguments to command
4c208a0 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Nov 22, 2021
@bernt-matthias
add missing arguments to command
540beea 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
@gallardoalba
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gallardoalba commented Nov 22, 2021 •
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In the case of SALSA2, I think that only this lines should be removed https://github.com/galaxyproject/tools-iuc/blob/master/tools/salsa2/salsa2.xml#L92 https://github.com/galaxyproject/tools-iuc/blob/master/tools/salsa2/salsa2.xml#L85

@gallardoalba
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In the case of USHER, the parameter of this test should be replaced by retain_input_branch_length, but the rest is fine https://github.com/galaxyproject/tools-iuc/blob/master/tools/usher/usher.xml#L302

@bernt-matthias
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but the rest is fine

Which rest do you mean?

@gallardoalba
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but the rest is fine

Which rest do you mean?

I mean, the correct name of this parameter is retain_input_branch_lengths; only this test should be modified.

bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Nov 23, 2021
@bernt-matthias
add missing arguments to command
7ccb4d4 
--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in galaxyproject#3704

xref galaxyproject#4095
bgruening pushed a commit that referenced this issue Nov 27, 2021
@bernt-matthias
cutadapt: add missing arguments and remove unsued test params (#4195)
9ec830a 
* cutadapt: remove absent read_modification

this was once the select of a conditional which was removed in
9a3d1b1

* same for output_filtering

* add missing arguments to command

--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in #3704

xref #4095
bernt-matthias added a commit to bernt-matthias/tools-iuc that referenced this issue Dec 3, 2021
@bernt-matthias
fix unused inputs
dc8097d 
kmerfilter: barcode_encoding in inputs but unused
populations: fastphase present in inputs but unused
shortreads: add_log used in test but absent from inputs

xref galaxyproject#4095
bernt-matthias added a commit to gallardoalba/tools-iuc that referenced this issue Apr 13, 2022
@bernt-matthias
fix unused inputs
2096fa0 
kmerfilter: barcode_encoding in inputs but unused
populations: fastphase present in inputs but unused
shortreads: add_log used in test but absent from inputs

xref galaxyproject#4095
bernt-matthias added a commit that referenced this issue Apr 14, 2022
@gallardoalba @bernt-matthias
Update Stacks2 (#4316)
16654f3 
* Update stack2

* Remove unnecesary macros

* Capitalize terms

* Fix macros for compatibility with stacks shortreads

* Fix command line

* Fix tag mismatch

* Update tests

* Fix test

* Include_comments

* Include delta

* Update failing test

* Fix datatype

* Update outputdata

* Fix test

* fix unused inputs

kmerfilter: barcode_encoding in inputs but unused
populations: fastphase present in inputs but unused
shortreads: add_log used in test but absent from inputs

xref #4095

* update version tokens

Co-authored-by: Cristóbal Gallardo <[email protected]>
Co-authored-by: Matthias Bernt <[email protected]>
@bernt-matthias bernt-matthias mentioned this issue Jan 27, 2023
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@bernt-matthias bernt-matthias mentioned this issue Feb 25, 2023
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@bernt-matthias bernt-matthias mentioned this issue Jan 19, 2024
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@bernt-matthias @gallardoalba