Hyphy tool updates (2.5.81) #7310
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This commit introduces several enhancements to the HyPhy tools:
- **Markdown Reports:** The `aBSREL` and `SLAC` tools now generate a markdown report with a summary of the analysis results.
- **Parameter Refactoring:**
- The genetic code and kill-zero-lengths parameters have been refactored into reusable macros.
- The `resample` macro help text has been clarified.
- **Profile Update:** The tool profile version has been updated to 24.0.
- **Command Updates:** The `SLAC` tool now uses `@HYPHYMP@` for execution.
- **Help Text:** The help sections for `aBSREL` and `SLAC` have been expanded and improved.
This commit introduces several enhancements to the `hyphy_fel.xml` tool: - Adds a markdown report to the output. - Adds support for intermediate fits output. - Expands the help section with more details on the tool and its options. - Adds more tests to cover new functionality and improve coverage. - Adds more parameters to the input, including support for multiple hits, site restriction, and more. - Fixes linting errors and inconsistencies in the tool definition.
This commit introduces several enhancements to the `hyphy_meme.xml` tool: - Adds a markdown report to the output. - Adds support for several new parameters, including `rates`, `multiple-hits`, `site-multihit`, `impute-states`, `precision`, `intermediate-fits`, `kill-zero-lengths`, `limit-to-sites`, and `save-lf-for-sites`. - Expands the help section to document the new options. - Updates the tests to include a new test and check for the new markdown output. - Redirects stderr to /dev/null to prevent it from being included in the markdown output.
This commit introduces several enhancements to the `hyphy_meme.xml` tool: - Adds a markdown report to the output. - Adds support for several new parameters, including `rates`, `multiple-hits`, `site-multihit`, `impute-states`, `precision`, `intermediate-fits`, `kill-zero-lengths`, `limit-to-sites`, and `save-lf-for-sites`. - Expands the help section to document the new options. - Updates the tests to include new tests and check for the new markdown output. - Fixes the conditional for the `branches` parameter in the tests. - Redirects stderr to /dev/null to prevent it from being included in the markdown output.
This commit introduces several enhancements to the `hyphy_bgm.xml` tool: - Updates the command to use correct argument names and the `--output` parameter. - Adds a markdown report to the output. - Adds new tests for protein and nucleotide alignments. - Updates the existing test to be a codon test. - Expands the help section with more details on the BGM method and its parameters. - Redirects stderr to /dev/null to prevent it from being included in the markdown output.
This commit introduces minor tweaks to the tests in `hyphy_bgm.xml` to make them more robust to small variations in output. - The delta for the file size check in the first test is increased. - The text assertion for the markdown report in the second test is made less specific.
This commit introduces a series of enhancements to the `hyphy_busted` Galaxy tool and the shared `macros.xml` file. The `hyphy_busted` tool has been updated to: - Add support for all command-line parameters, including the new MSS (multiple synonymous rate class substitutions) feature. - Improve the help section with a more detailed description of the methodology and a complete list of all parameter options. - Add a markdown report output that captures the standard output of the tool. - Add more tests to cover the new functionality. - Fix all linting issues. The `macros.xml` file has been updated to: - Create a new `busted_advanced_options` macro to separate the advanced options for BUSTED from the other tools. - Add help text to all parameters. - Improve the structure of the conditionals for better user experience.
This commit introduces a series of enhancements to the `hyphy_gard` Galaxy tool and updates the shared `macros.xml` file. The `hyphy_gard` tool has been updated to: - Add support for `max-breakpoints` and `mode` parameters. - Create an advanced settings block for more esoteric parameters. - Improve the help section with a more detailed description of the methodology and a complete list of all parameter options. - Add a markdown report output that captures the standard output of the tool. - Update the tests to cover the new functionality and fix linting issues. - Add inline help text to all parameters. The `macros.xml` file has been updated to: - Update the `@TOOL_VERSION@` token to `2.5.81`. - Update the `substitution` macro to include the elucidated protein models and set JTT as the default. - Add inline help text to the parameters in the `conditional_posteriorEstimationMethod` and `mcmc_options` macros.
This commit reworks the `hyphy_annotate` Galaxy tool to use the `hyphy label-tree` command instead of the custom `annotator.bf` script. The `hyphy_annotate` tool has been updated to: - Use `hyphy label-tree` for tree annotation. - Update inputs to reflect `label-tree` parameters, including options for selection method (regexp or list), rerooting, inversion, and internal/leaf node labeling strategies. - Simplify outputs to a single labeled Newick tree and a markdown report. - Update the test to match the new functionality. - Update the help section with a detailed description of the `label-tree` method and its parameters. - Add inline help text to all parameters.
This commit introduces a series of enhancements to the `hyphy_fade` Galaxy tool. The `hyphy_fade` tool has been updated to: - Create an advanced settings block for `grid` and `concentration_parameter`. - Improve the help section with a more detailed description of the methodology and a complete list of all parameter options. - Add a markdown report output that captures the standard output of the tool. - Update the tests to cover the new functionality and fix linting issues. - Add inline help text to all parameters. - Adjust the test to use the WAG model.
This commit introduces a series of improvements and fixes to the hyphy-relax Galaxy tool. - Refactored the command generation for multiple-file analysis to use a filelist, and corrected alignment path for single-file analysis. - Added four new test cases to cover different modes and options (multiple files, HMM, Group mode). - Updated all tests to use explicit conditional parameter definitions and robust output assertions (file size and content checks). - Significantly improved the help section with detailed explanations of the method, input formats, and all tool options. - Made the 'reference-group' parameter conditional on 'Group mode'. - Added missing '--starting-points' and '--grid-size' parameters to the advanced options macros. - Fixed all outstanding linting issues reported by planemo. - Added and modified input test data files to support the new and updated tests.
This commit introduces a series of improvements and fixes to the hyphy_prime Galaxy tool. - Added support for custom property files, intermediate fits output, and kill-zero-lengths option. - Expanded the available property sets with Random-* options. - Refactored the input parameters to be more user-friendly, using conditionals to show relevant options. - Created a comprehensive test suite with four tests covering different options and modes. - Added robust assertions to all tests for file size and content. - Significantly improved the help section with detailed explanations of the method, all parameters, and a new section on multiple file analysis. - Fixed all linting issues reported by planemo. - Hid the 'save_intermediate' parameter from the user.
This commit introduces a series of improvements and fixes to the hyphy_sm19 Galaxy tool. - Updated command invocation to use '@hyphy@ sm' for a more direct call. - Added '--weight' and '--use-bootstrap' parameters to the tool's inputs. - Corrected the '--groups' argument to properly evaluate the length of partitions. - Added redirection for stdout to 'sm19_stdout.md' for capturing markdown reports. - Expanded the help section with more detailed methodology and intuition. - Added inline help messages to all parameters. - Fixed all linting issues reported by planemo.
This commit removes the generated test output files for hyphy_sm19, as requested.
This commit introduces a series of improvements and fixes to the hyphy_strike_ambigs Galaxy tool.
- Added the '--code' parameter (via the 'gencode' macro) to the tool's inputs.
- Updated the command template to pass the '--code' argument and to redirect stdout to a markdown report.
- Enhanced the test suite with robust assertions for file size and specific content in both the FASTA output and the new Markdown report.
- Updated the input file for Test 1 ('strike-ambigs-in1.fa') with 10 randomly selected sequences from 'HIV_RT.nex'.
- Expanded the help section with a clearer explanation of the tool's function, input requirements, and all tool options.
- Added inline help messages to all parameters.
- Fixed all linting issues reported by planemo.
This commit removes the generated test output files for hyphy_strike_ambigs, as requested.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
FOR CONTRIBUTOR: