# HG changeset patch
# User iuc
# Date 1764088872 0
# Node ID 1ac4a5f05f336e0f38fa2124831c33dda38c36f9
# Parent 05bd4db20227587b3ed103a358eb2b817a2a7066
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
diff -r 05bd4db20227 -r 1ac4a5f05f33 macros.xml
--- a/macros.xml Thu Nov 07 13:07:52 2024 +0000
+++ b/macros.xml Tue Nov 25 16:41:12 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 05bd4db20227 -r 1ac4a5f05f33 plotting.xml
--- a/plotting.xml Thu Nov 07 13:07:52 2024 +0000
+++ b/plotting.xml Tue Nov 25 16:41:12 2025 +0000
@@ -7,30 +7,31 @@
@@ -67,30 +62,31 @@
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@@ -102,6 +98,9 @@
method['out_file'] == 'svg'
+
+ method['out_file'] == 'html'
+
advanced_common['show_log']
@@ -111,20 +110,20 @@
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`__
+`__
Plot the UMAP embedding, using `pl.umap`
========================================
@@ -220,7 +226,7 @@
Plot the UMAP embedding.
More details on the `SnapATAC2 documentation
-`__
+`__
Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues`
===========================================================================
@@ -228,7 +234,7 @@
Plot the eigenvalues of spectral embedding.
More details on the `SnapATAC2 documentation
-`__
+`__
]]>
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue Nov 25 16:41:12 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 Human (hg38) ${__HERE__}/chr21_small.fasta.gz
\ No newline at end of file
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/chr21.gff3.gz
Binary file test-data/chr21.gff3.gz has changed
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/chr21_small.fasta.gz
Binary file test-data/chr21_small.fasta.gz has changed
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/cisBP_human.meme.gz
Binary file test-data/cisBP_human.meme.gz has changed
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/gene_sets.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_sets.loc Tue Nov 25 16:41:12 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 hg38GFF ${__HERE__}/chr21.gff3.gz
\ No newline at end of file
diff -r 05bd4db20227 -r 1ac4a5f05f33 test-data/meme.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme.loc Tue Nov 25 16:41:12 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 05bd4db20227 -r 1ac4a5f05f33 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 16:41:12 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 05bd4db20227 -r 1ac4a5f05f33 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 16:41:12 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 05bd4db20227 -r 1ac4a5f05f33 tool-data/meme.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/meme.loc.sample Tue Nov 25 16:41:12 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 05bd4db20227 -r 1ac4a5f05f33 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 16:41:12 2025 +0000
@@ -0,0 +1,17 @@
+
+
+
+ value, dbkey, name, path
+
+
+
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+ value, dbkey, name, path
+
+
+
+
+
\ No newline at end of file
diff -r 05bd4db20227 -r 1ac4a5f05f33 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 16:41:12 2025 +0000
@@ -0,0 +1,14 @@
+
+
+ value, dbkey, name, path
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+ value, dbkey, name, path
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+
\ No newline at end of file