# HG changeset patch
# User iuc
# Date 1764088798 0
# Node ID 2c289e3b566abd08a897ee06e48875368f1d2522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
diff -r 000000000000 -r 2c289e3b566a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Nov 25 16:39:58 2025 +0000
@@ -0,0 +1,256 @@
+
+ 2.8.0
+ 0
+ 24.0
+
+
+ snapatac
+
+
+
+ snapatac2
+ hdbscan
+ leidenalg
+ umap-learn
+ xgboost
+ python-kaleido
+ polars
+ plotly
+ python-kaleido
+ harmonypy
+ scanorama
+
+
+
+
+
+ '$hidden_output' &&
+ python '$script_file' >> '$hidden_output' &&
+ touch 'anndata_info.txt' &&
+ cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
+ ]]>
+
+
+ fasta.fa &&
+ echo "Using built-in FASTA: '$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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+ 10.1038/s41592-023-02139-9
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diff -r 000000000000 -r 2c289e3b566a network.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/network.xml Tue Nov 25 16:39:58 2025 +0000
@@ -0,0 +1,397 @@
+
+ analysis
+
+ macros.xml
+
+
+
+
+
+ 'input.meme' &&
+ #if $gff_file_condi.gffSource == 'cached':
+ ln -s '$gff_file_condi.gff_pre_installed.fields.path' anno.gff &&
+ #else:
+ ln -s '$gff_file_condi.gff_history' anno.gff &&
+ #end if
+ #if $fasta_file_condi.fastaSource == 'indexed':
+ zcat '$fasta_file_condi.fasta_pre_installed.fields.path' > fasta.fa &&
+ #else:
+ zcat '$fasta_file_condi.fasta_history' > fasta.fa &&
+ #end if
+ mkdir -p network_dir &&
+ cp '$adata_rna' 'anndata_rna.h5ad' &&
+ cp '$adata_atac' 'anndata_atac.h5ad' &&
+@CMD@
+ ]]>
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+ advanced_common['show_log']
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+ out_file != 'svg' and out_file != 'html'
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+ out_file == 'svg'
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+ out_file == 'html'
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+ `__
+
+
+Compute correlation scores for any two connected nodes in the network.
+
+More details on the `SnapATAC2 documentation
+`__
+
+
+Perform regression analysis for nodes and their parents in the network.
+
+More details on the `SnapATAC2 documentation
+`__
+
+
+Add TF motif binding information.
+
+More details on the `SnapATAC2 documentation
+`__
+
+ ]]>
+
+
+
diff -r 000000000000 -r 2c289e3b566a test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue Nov 25 16:39:58 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 Human (hg38) ${__HERE__}/chr21_small.fasta.gz
\ No newline at end of file
diff -r 000000000000 -r 2c289e3b566a test-data/chr21.gff3.gz
Binary file test-data/chr21.gff3.gz has changed
diff -r 000000000000 -r 2c289e3b566a test-data/chr21_small.fasta.gz
Binary file test-data/chr21_small.fasta.gz has changed
diff -r 000000000000 -r 2c289e3b566a test-data/cisBP_human.meme.gz
Binary file test-data/cisBP_human.meme.gz has changed
diff -r 000000000000 -r 2c289e3b566a test-data/gene_sets.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_sets.loc Tue Nov 25 16:39:58 2025 +0000
@@ -0,0 +1,1 @@
+hg38 hg38 hg38GFF ${__HERE__}/chr21.gff3.gz
\ No newline at end of file
diff -r 000000000000 -r 2c289e3b566a test-data/meme.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme.loc Tue Nov 25 16:39:58 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 000000000000 -r 2c289e3b566a 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 16:39:58 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 000000000000 -r 2c289e3b566a 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 16:39:58 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 000000000000 -r 2c289e3b566a tool-data/meme.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/meme.loc.sample Tue Nov 25 16:39:58 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 000000000000 -r 2c289e3b566a 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 16:39:58 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 000000000000 -r 2c289e3b566a 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 16:39:58 2025 +0000
@@ -0,0 +1,14 @@
+
+
+ value, dbkey, name, path
+
+
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+ value, dbkey, name, path
+
+
+
+
\ No newline at end of file