# HG changeset patch
# User iuc
# Date 1764088879 0
# Node ID 02a7162fc510d35aa7bc5e7ac9310309d16d2fa9
# Parent 64fa083411f175dcc4428026afce1d6a08083f02
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
diff -r 64fa083411f1 -r 02a7162fc510 macros.xml
--- a/macros.xml Thu Nov 07 13:07:55 2024 +0000
+++ b/macros.xml Tue Nov 25 16:41:19 2025 +0000
@@ -1,7 +1,7 @@
- 2.6.4
- 1
- 23.0
+ 2.8.0
+ 0
+ 24.0
snapatac
@@ -9,168 +9,74 @@
snapatac2
- plotly
- python-kaleido
- polars
- pyarrow
- python-igraph
- hdbscan
- harmonypy
- scanorama
- macs3
- multiprocess
- leidenalg
+ hdbscan
+ leidenalg
+ umap-learn
+ xgboost
+ python-kaleido
+ polars
+ plotly
+ python-kaleido
+ harmonypy
+ scanorama
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+ ]]>
'$hidden_output' &&
python '$script_file' >> '$hidden_output' &&
touch 'anndata_info.txt' &&
- cat 'anndata_info.txt' @CMD_prettify_stdout@
- ]]>
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+ fasta.fa &&
+ echo "Using built-in FASTA: '$method.fasta_file_condi.fasta_pre_installed.fields.name'" >&2 &&
+ #else:
+ #if $method.fasta_file_condi.fasta_history.ext.endswith('.gz')
+ zcat '$method.fasta_file_condi.fasta_history' > fasta.fa &&
+ #else:
+ ln -s '$method.fasta_file_condi.fasta_history' fasta.fa &&
+ #end if
+ #end if
]]>
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diff -r 64fa083411f1 -r 02a7162fc510 peaks_and_motif_analysis.xml
--- a/peaks_and_motif_analysis.xml Thu Nov 07 13:07:55 2024 +0000
+++ b/peaks_and_motif_analysis.xml Tue Nov 25 16:41:19 2025 +0000
@@ -9,22 +9,34 @@
'input.meme' &&
+#end if
+#if $method.method == 'tl.marker_regions' and str($method.enrichment_condi.motif_enrichment) == "yes":
+@CMD_GET_FASTA@
+#end if
+#if $method.method != 'pp.merge_peaks'
+@CMD_PREP_ADATA@
+#end if
@CMD@
]]>
@@ -166,9 +213,11 @@
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+ method['method'] != 'tl.marker_regions' and method['method'] != 'tl.diff_test'
+
advanced_common['show_log']
@@ -253,6 +337,21 @@
(method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'svg'
+
+ (method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'html'
+
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+ (method['method'] == 'tl.marker_regions' and method['enrichment_condi']['motif_enrichment'] == 'yes') and method['enrichment_condi']['out_file'] == 'png'
+
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+ (method['method'] == 'tl.marker_regions' and method['enrichment_condi']['motif_enrichment'] == 'yes') and method['enrichment_condi']['out_file'] == 'pdf'
+
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+ (method['method'] == 'tl.marker_regions' and method['enrichment_condi']['motif_enrichment'] == 'yes') and method['enrichment_condi']['out_file'] == 'svg'
+
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+ (method['method'] == 'tl.marker_regions' and method['enrichment_condi']['motif_enrichment'] == 'yes') and method['enrichment_condi']['out_file'] == 'html'
+
method['method'] == 'tl.diff_test'
@@ -262,7 +361,7 @@
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`__
+`__
Merge peaks from different groups, using `tl.merge_peaks`
=========================================================
@@ -457,19 +695,16 @@
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.
+Generate cell by peak count matrix, using `pp.make_peak_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.
+This function will generate a cell by peak count matrix.
+`import_fragments` 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`
======================================================================
@@ -477,7 +712,7 @@
A quick-and-dirty way to get marker regions.
More details on the `SnapATAC2 documentation
-`__
+`__
Identify differentially accessible regions, using `tl.diff_test`
====================================================================
@@ -485,7 +720,7 @@
Identify differentially accessible regions.
More details on the `SnapATAC2 documentation
-`__
+`__
]]>
diff -r 64fa083411f1 -r 02a7162fc510 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 Human (hg38) ${__HERE__}/chr21_small.fasta.gz
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 test-data/chr21.gff3.gz
Binary file test-data/chr21.gff3.gz has changed
diff -r 64fa083411f1 -r 02a7162fc510 test-data/chr21_small.fasta.gz
Binary file test-data/chr21_small.fasta.gz has changed
diff -r 64fa083411f1 -r 02a7162fc510 test-data/cisBP_human.meme.gz
Binary file test-data/cisBP_human.meme.gz has changed
diff -r 64fa083411f1 -r 02a7162fc510 test-data/gene_sets.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_sets.loc Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 hg38GFF ${__HERE__}/chr21.gff3.gz
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 test-data/meme.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme.loc Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,1 @@
+cisbp snap.datasets.cis_bp(unique=True) ${__HERE__}/cisBP_human.meme.gz
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,17 @@
+#This file lists the locations and dbkeys of all the genome and transcriptome fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel4.5 apiMel4.5 Honeybee (Apis mellifera): apiMel4.5 /path/to/genome/apiMel4.5/apiMel4.5.fa
+#hg38canon hg38 Human (Homo sapiens): hg38 Canonical /path/to/genome/hg38/hg38canon.fa
+#hg38full hg38 Human (Homo sapiens): hg38 Full /path/to/genome/hg38/hg38full.fa
+#hg38full.90 hg38 Human (Homo sapiens): hg38 Full Trans v90 /path/to/genome/hg38/hg38fulltrans.fa
+
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg38 above.
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 tool-data/gene_sets.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_sets.loc.sample Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,14 @@
+# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format.
+#
+# The gene_sets.loc file syntax is:
+#
+#
+# Please ensure that the above fields are tab separated.
+#
+# In case you have TWO or MORE providers PER dbkey, the one mentioned
+# first in the file, should have the "default" priority.
+#
+#Example:
+#
+#Homo_sapiens.GRCh38.90 hg38 GRCh38 (hg38) annotation from Ensembl, release 90 /depot/data2/galaxy/hg38/gene_sets/Homo_sapiens.GRCh38.90.gtf
+#Homo_sapiens.GRCh37.87 hg19 GRCh37 (hg19) annotation from Ensembl, release 87 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.87.gtf
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 tool-data/meme.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/meme.loc.sample Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,13 @@
+# This is a sample file distributed with snapatac2 which enables the tool to perform motif enrichment analysis
+#
+# The meme.loc file syntax is:
+#
+#
+# Please ensure that the above fields are tab separated.
+#
+# Currently the files should be downloaded manually
+#
+#Example:
+#
+#cisbp cis_bp(unique=True) /path/to/cisBP_human.meme.gz
+#meuleman_2020 Meuleman_2020 /path/to/Meuleman_2020.meme.gz
\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,17 @@
+
+
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+ value, dbkey, name, path
+
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+ value, dbkey, name, path
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\ No newline at end of file
diff -r 64fa083411f1 -r 02a7162fc510 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Nov 25 16:41:19 2025 +0000
@@ -0,0 +1,14 @@
+
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+ value, dbkey, name, path
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+ value, dbkey, name, path
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\ No newline at end of file