# HG changeset patch
# User iuc
# Date 1716477590 0
# Node ID 1c52ce6225900b387169ea78a8a5fb4c3151b121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
diff -r 000000000000 -r 1c52ce622590 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 23 15:19:50 2024 +0000
@@ -0,0 +1,190 @@
+
+ 2.5.3
+ 1
+ 23.0
+
+ snapatac2
+ plotly
+ python-kaleido
+ polars
+ pyarrow
+ python-igraph
+ hdbscan
+ harmonypy
+ scanorama
+ macs3
+ multiprocess
+ leidenalg
+
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+
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+ '$hidden_output' &&
+ python '$script_file' >> '$hidden_output' &&
+ touch 'anndata_info.txt' &&
+ cat 'anndata_info.txt' @CMD_prettify_stdout@
+ ]]>
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+ 10.1038/s41592-023-02139-9
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diff -r 000000000000 -r 1c52ce622590 peaks_and_motif_analysis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peaks_and_motif_analysis.xml Thu May 23 15:19:50 2024 +0000
@@ -0,0 +1,485 @@
+
+ analysis
+
+ macros.xml
+
+
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+ $method.cutoff_l2fc)['feature name'].to_numpy(),
+ group2: diff_peaks.filter(polars.col("log2(fold_change)") < $method.cutoff_l2fc)['feature name'].to_numpy(),
+ }
+ #else if $method.compare.with == 'background_group'
+peaks_to_plot = {
+ group1: diff_peaks['feature name'].to_numpy()
+ }
+ #end if
+
+sa.pl.regions(
+ adata,
+ groupby = group_key,
+ peaks = peaks_to_plot,
+ @CMD_params_render_plot@
+)
+
+#end if
+@CMD_anndata_write_outputs@
+ ]]>
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+ advanced_common['show_log']
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+ method['method'] == 'tl.merge_peaks'
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+ (method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'png'
+
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+ (method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'pdf'
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+ (method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'svg'
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+ method['method'] == 'tl.diff_test'
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+ `__
+
+Merge peaks from different groups, using `tl.merge_peaks`
+=========================================================
+
+Merge peaks from different groups.
+
+Merge peaks from different groups. It is typically used to merge results from `macs3`.
+
+This function initially expands the summits of identified peaks by `half_width` on both sides. Following this expansion, it addresses the issue of overlapping peaks through an iterative process. The procedure begins by prioritizing the most significant peak, determined by the smallest p-value. This peak is retained, and any peak that overlaps with it is excluded. Subsequently, the same method is applied to the next most significant peak. This iteration continues until all peaks have been evaluated, resulting in a final list of non-overlapping peaks, each with a fixed width determined by the initial extension.
+
+More details on the `SnapATAC2 documentation
+`__
+
+Generate cell by bin count matrix, using `pp.add_tile_matrix`
+=============================================================
+
+Generate cell by bin count matrix.
+
+This function is used to generate and add a cell by bin count matrix to the AnnData object.
+
+`import_data` must be ran first in order to use this function.
+
+More details on the `SnapATAC2 documentation
+`__
+
+A quick-and-dirty way to get marker regions, using `tl.marker_regions`
+======================================================================
+
+A quick-and-dirty way to get marker regions.
+
+More details on the `SnapATAC2 documentation
+`__
+
+Identify differentially accessible regions, using `tl.diff_test`
+====================================================================
+
+Identify differentially accessible regions.
+
+More details on the `SnapATAC2 documentation
+`__
+ ]]>
+
+
+