Fix SnapATAC2 gene activity matrix bug (galaxyproject#6109)

* Fix SnapATAC2 gene activity matrix bug * bump version suffix * update test data
Bio2Byte · Jul 5, 2024 · df9c285 · df9c285
1 parent 091caba
commit df9c285
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/tools/snapatac2/macros.xml b/tools/snapatac2/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>

diff --git a/tools/snapatac2/preprocessing.xml b/tools/snapatac2/preprocessing.xml
@@ -91,7 +91,7 @@ sa.pp.add_tile_matrix(
 )
 
 #else if $method.method == 'pp.make_gene_matrix'
-sa.pp.make_gene_matrix(
+adata = sa.pp.make_gene_matrix(
     adata,
     gene_anno = '$method.gene_anno',
     chunk_size = $method.chunk_size,
@@ -464,7 +464,7 @@ sa.metrics.tsse(
                     <has_text_matching expression="count_frag_as_reads = True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
         </test>
         <test expect_num_outputs="2">
             <!-- metrics.tsse -->