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feat: Deeptools plot correlation (#3137)
<!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> <!-- Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced `environment.linux-64.pin.txt` for consistent Conda environment setup on Linux 64-bit. - Added `environment.yaml` for configuring Conda environment with DeepTools dependencies. - Launched `meta.yaml` providing essential metadata for the Deeptools Plot Correlation tool. - Created a Snakemake rule for testing correlation plot generation. - Developed `wrapper.py` to facilitate plotting with customizable parameters. - Implemented a new test function for validating plot correlation functionality. - **Documentation** - Enhanced documentation within new files to support user setup and usage instructions. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: tdayris <tdayris@gustaveroussy.fr> Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder <felix.moelder@uni-due.de> Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>
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bio/deeptools/plotcorrelation/environment.linux-64.pin.txt
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| # This file may be used to create an environment using: | ||
| # $ conda create --name <env> --file <this file> | ||
| # platform: linux-64 | ||
| @EXPLICIT | ||
| https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 | ||
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| https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce | ||
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| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - nodefaults | ||
| dependencies: | ||
| - deeptools =3.5.5 |
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| name: Deeptools Plot Correlation | ||
| url: https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html | ||
| description: > | ||
| Analysis and visualization of sample correlations based on the output of multiBamSummary or multiBigwigSummary. | ||
| authors: | ||
| - Thibault Dayris | ||
| input: | ||
| - Path to compressed matrix file | ||
| output: | ||
| - plot: Path to scatterplot/heatmap. The available formats are `.png`, `.eps`, `.pdf` and `.svg` | ||
| - matrix: Optional path to pairwise correlation values (TSV) | ||
| params: | ||
| - extra: Optional parameters except IO and `--plotFileFormat`. | ||
| - correlation: Either `spearman`, or `pearson`. No default is set in DeepTools. This wrapper considers `spearman` as default value. | ||
| - plot: Either `heatmap`, or `scatterplot`. No default is set in DeepTools. This wrapper considers `heatmap` as default value. | ||
| notes: | | ||
| Plot file format is automatically inferred from plot file extension. |
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| rule test_deeptools_plot_correlation: | ||
| input: | ||
| "bins.npz", | ||
| output: | ||
| plot="bins.svg", | ||
| counts="counts.tsv", # Optional output file | ||
| threads: 1 | ||
| params: | ||
| extra="--skipZeros", # Any optional parameters besides IO and --plotFileFormat | ||
| correlation="spearman", # either spearman or pearson | ||
| plot="heatmap", # either heatmap or scatterplot | ||
| log: | ||
| "corr.log", | ||
| wrapper: | ||
| "master/bio/deeptools/plotcorrelation" |
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| # coding: utf-8 | ||
|
|
||
| __author__ = "Thibault Dayris" | ||
| __copyright__ = "Copyright 2024, Thibault Dayris" | ||
| __email__ = "thibault.dayris@gustaveroussy.fr" | ||
| __license__ = "MIT" | ||
|
|
||
|
|
||
| from snakemake.shell import shell | ||
|
|
||
| # Optional parameters | ||
| log = snakemake.log_fmt_shell(stdout=True, stderr=True) | ||
| extra = snakemake.params.get("extra", "") | ||
|
|
||
| # Get required arguments | ||
| cor_method = snakemake.params.get("correlation", "spearman") | ||
| what_to_plot = snakemake.params.get("plot", "heatmap") | ||
|
|
||
| # Get plot file format | ||
| fmt = str(snakemake.output["plot"]).split(".")[-1].lower() | ||
|
|
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| # Get optional output matrix | ||
| corr_matrix = snakemake.output.get("counts") | ||
| if corr_matrix: | ||
| extra += f" --outFileCorMatrix {corr_matrix} " | ||
|
|
||
| shell( | ||
| "plotCorrelation " | ||
| "--corData {snakemake.input[0]} " | ||
| "--corMethod {cor_method} " | ||
| "--whatToPlot {what_to_plot} " | ||
| "--plotFile {snakemake.output.plot} " | ||
| "--plotFileFormat {fmt} " | ||
| "{extra} {log}" | ||
| ) |
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