# HG changeset patch # User iuc # Date 1738752805 0 # Node ID 678260997e94a4594aeed7120bb508a46e327321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ commit bcf2ec32c3d13b29da55e0e638da7ddd7162c436 diff -r 000000000000 -r 678260997e94 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 05 10:53:25 2025 +0000 @@ -0,0 +1,264 @@ + + 0.1.6 + 0 + 23.0 + + + muon + leidenalg + louvain + mofapy2 + + + + + muon + + + + + + + + + + 10.1186/s13059-021-02577-8 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + '$hidden_output' && +python '$script_file' >> '$hidden_output' && +touch 'mudata_info.txt' && +cat 'mudata_info.txt' @CMD_prettify_stdout@ + ]]> + + + + + + + + +
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+ + + advanced_common['show_log'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
diff -r 000000000000 -r 678260997e94 preprocess_muon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess_muon.xml Wed Feb 05 10:53:25 2025 +0000 @@ -0,0 +1,322 @@ + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ `__ + +Filter: Filter variables (features) ('muon.pp.filter_var') +========================================================== + + Filter variables (features, e.g. genes) in-place using any column in .var or row in .X. + + More details on the `muon documentation + `__ + +Subset: Subset observations (samples or cells) in-place taking observations present only in all modalities ('muon.pp.intersect_obs') +==================================================================================================================================== + + Subset observations (samples or cells) in-place taking observations present only in all modalities. + + More details on the `muon documentation + `__ + +Normalize: Normalize observations to unit L2 norm ('muon.pp.l2norm') +==================================================================== + + Normalize observations to unit L2 norm. + + More details on the `muon documentation + `__ + +Search: Multimodal nearest neighbor search ('muon.pp.neighbors') +================================================================ + + Multimodal nearest neighbor search by implementing the multimodal nearest neighbor method of Hao et al. and Swanson et al. + The neighbor search efficiency on this heavily relies on UMAP. In particular, you may want to decrease + n_multineighbors for large data set to avoid excessive peak memory use. To achieve results as close as possible + to the Seurat implementation, observations must be normalized to unit L2 norm prior to running per-modality + nearest-neighbor search. + + More details on the `muon documentation + `__ + + ]]> + +
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