Constava #7328
Constava #7328
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Add constava
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Tool tests are failing on the exact same step as #7243 (See GH action run) so I suspect there is an issue with the CI/CD of the repository perhaps? |
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Indeed @B0r1sD, in my local workstation the tests are all green with the command provided by the contributing guidelines as well as the planemo lint: Lint: planemo lint ./tools/constava/constava.xml
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.. CHECK (TestsNoValid): 12 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 17 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [constava].
.. CHECK (ToolNameValid): Tool defines a name [Constava].
.. CHECK (ToolProfileValid): Tool specifies profile version [24.2].
.. CHECK (ToolVersionValid): Tool defines a version [1.1.0+galaxy0].
.. INFO (CommandInfo): Tool contains a command.
.. CHECK (CitationsFound): Found 2 citations. Tests: planemo test --install_galaxy tools/constava/constava.xml
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All 12 test(s) executed passed.
constava (Test #1): passed
constava (Test #2): passed
constava (Test #3): passed
constava (Test #4): passed
constava (Test #5): passed
constava (Test #6): passed
constava (Test #7): passed
constava (Test #8): passed
constava (Test #9): passed
constava (Test #10): passed
constava (Test #11): passed
constava (Test #12): passedIs there anything that we could change from our side to fix the CI/CD pipeline @bgruening ? Thanks in advance |
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Please test with |
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Hello there, thanks for the feedback. Everything must be resolved now. Test passed in the CI/CD but the same error at the step that checks the test status. Locally linter and tests are passing green: 
Any hints ? Could it be related to any project related naming in the files ? |
No, unfortunately we are experiencing some CI issues lately. Nonetheless, we re-trigger the failed workflow manually :) Should be green now. |
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Thanks @SaimMomin12 for the info ! Let us know if the PR needs more changes. We're looking forward to seeing Constava on Galaxy soon 🚀 Kind regards from Brussels to you all |
tools/constava/constava.xml
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| <environment_variable name="PYTHON_TQDM_DISABLE">1</environment_variable> | ||
| </environment_variables> | ||
| <inputs> | ||
| <section name="input_options" title="Input Options" expanded="true" help="As input data the backbone dihedral angles extracted from the conformational ensemble need to be provided. Important: Given Constava extracts RESNAME and RESINDEX from filenames when using XVG format, your files must follow this regex 'ramaPhiPsi([A-Z][A-Z0-9][A-Z0-9])([0-9]+).xvg'"> |
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should this help section be really at the section level?
It would fit better at the format=data level I think?
Please also consider to rephrase it. Its not a filename in the Galaxy context, but rather the dataset name, that a user can change :(
tools/constava/constava.xml
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| <option value="bootstrap">Bootstrap sampling</option> | ||
| </param> | ||
| <when value="window"> | ||
| <param name="window_size" type="text" label="Window size (space-separated integers)" value="3" help="Specify window sizes for moving frame analysis, e.g., '3 5 7'. Each reading frame consists of consecutive samples. Multiple values can be provided."/> |
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you could add here a "validator" that checks that the input is really just numbers and spaces
tools/constava/constava.xml
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| <param name="window_size" type="text" label="Window size (space-separated integers)" value="3" help="Specify window sizes for moving frame analysis, e.g., '3 5 7'. Each reading frame consists of consecutive samples. Multiple values can be provided."/> | ||
| </when> | ||
| <when value="bootstrap"> | ||
| <param name="bootstrap_size" type="text" label="Bootstrap size (space-separated integers)" value="3" help="Do inference using N samples obtained through bootstrapping. Specify bootstrap sizes, e.g., '10 20 30'. Samples obtained through bootstrapping. Multiple values can be provided."/> |
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some here a validator would be nice
Co-authored-by: Björn Grüning <[email protected]>
All are useful comments, thank you for your patience reviewing the PR @bgruening and @SaimMomin12. CI/CD passed green, would you mind if I asked for a new review round ? |
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Let's ship it :) If you feel like it: https://galaxyproject.eu/posts/2020/08/22/three-steps-to-galaxify-your-tool/ |
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Thank you so much reviewers for your patience and guidance!!! I'll open the PR in |
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Here it is: usegalaxy-eu/usegalaxy-eu-tools#921 |
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Thanks a lot @agdiaz. Great work! |
5 participants
FOR CONTRIBUTOR:
Original PR that contains all information about the tool by @agdiaz: #6235. As that repo was archived, making a new PR was necessary.
@agdiaz feel free to add any additional information, in addition to your original, elaborative PR.