--- a/macros.xml	Wed Sep 22 21:10:58 2021 +0000
+++ b/macros.xml	Wed Nov 08 14:45:35 2023 +0000
@@ -1,12 +1,16 @@
 <macros>
-    <token name="@version@">1.7.1</token>
-    <token name="@profile@">19.01</token>
+    <token name="@version@">1.9.6</token>
+    <token name="@profile@">22.05</token>
     <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@version@">scanpy</requirement>
-            <requirement type="package" version="2.0.17">loompy</requirement>
-            <requirement type="package" version="0.8.3">leidenalg</requirement>
+            <requirement type="package" version="3.0.6">loompy</requirement>
+            <requirement type="package" version="0.10.1">leidenalg</requirement>
+            <requirement type="package" version="0.8.1">louvain</requirement>
+            <requirement type="package" version="1.5.3">pandas</requirement>
+            <requirement type="package" version="3.7">matplotlib</requirement>
+            <requirement type="package" version="0.12.2">seaborn</requirement>
             <yield />
         </requirements>
     </xml>
@@ -15,9 +19,15 @@
             <xref type="bio.tools">scanpy</xref>
         </xrefs>
     </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-017-1382-0</citation>
+            <citation type="doi">10.1093/gigascience/giaa102</citation>
         </citations>
     </xml>
     <xml name="version_command">
@@ -56,7 +66,7 @@
         <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
     </xml>
     <token name="@CMD_read_inputs@"><![CDATA[
-adata = sc.read('anndata.h5ad')
+adata = sc.read_h5ad('anndata.h5ad')
 ]]>
     </token>
     <xml name="inputs_common_advanced">
@@ -66,12 +76,12 @@
     </xml>
     <xml name="anndata_outputs">
         <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
-        <data name="hidden_output" format="txt" label="Log file" >
+            <data name="hidden_output" format="txt" label="Log file" >
             <filter>advanced_common['show_log']</filter>
         </data>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
-adata.write('anndata.h5ad')
+adata.write_h5ad('anndata.h5ad')
 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
     print(adata, file=ainfo)
 ]]>
@@ -875,7 +885,7 @@
     </xml>
     <xml name="param_color_map">
         <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
-            <option value="None">Default</option>
+            <option value="" >Default</option>
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -979,7 +989,7 @@
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
     @CMD_param_size@
-    #if str($method.plot.color_map) != 'None'
+    #if str($method.plot.color_map) != ''
     color_map='$method.plot.color_map',
     #end if
     #if str($method.plot.palette) != ''

--- a/remove_confounders.xml	Wed Sep 22 21:10:58 2021 +0000
+++ b/remove_confounders.xml	Wed Nov 08 14:45:35 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="scanpy_remove_confounders" name="Remove confounders" version="@galaxy_version@" profile="@profile@">
     <description>with scanpy</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@
@@ -122,7 +122,7 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 0 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
@@ -140,7 +140,7 @@
             </output>
             <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <!--<test>
+        <!--<test expect_num_outputs="2">
             < test 2 >
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
@@ -153,7 +153,7 @@
             </assert_stdout>
             <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>-->
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 1 -->
             <param name="adata" value="blobs.h5ad" />
             <conditional name="method">
@@ -180,7 +180,7 @@
 inspired by Seurat's `regressOut` function in R.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.regress_out.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.regress_out.html>`__
 
 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`
 ==================================================================================
@@ -191,7 +191,7 @@
 Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.api.pp.mnn_correct.html>`__
+<https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.mnn_correct.html>`__
 
 
 Correct batch effects with ComBat function (`pp.combat`)
@@ -200,7 +200,7 @@
 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.combat.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.combat.html>`__
 
 
     ]]></help>

Binary file test-data/blobs.h5ad has changed

Binary file test-data/krumsiek11.h5ad has changed

Binary file test-data/pbmc68k_reduced.h5ad has changed

Binary file test-data/pl.clustermap.krumsiek11.png has changed

Binary file test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed

Binary file test-data/pl.dotplot.krumsiek11.png has changed

Binary file test-data/pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed

Binary file test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed

Binary file test-data/pl.draw_graph.png has changed

Binary file test-data/pl.embedding_density.pbmc68k_reduced.png has changed

Binary file test-data/pl.heatmap.krumsiek11.png has changed

Binary file test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png has changed

Binary file test-data/pl.highly_variable_genes.seurat.blobs.png has changed

Binary file test-data/pl.matrixplot.krumsiek11.png has changed

Binary file test-data/pl.paga.paul15_gauss_braycurtis.png has changed

Binary file test-data/pl.paga_compare.paul15_gauss_braycurtis.png has changed

Binary file test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf has changed

Binary file test-data/pl.pca_loadings.pp.pca.krumsiek11.png has changed

Binary file test-data/pl.pca_overview.pp.pca.krumsiek11.png has changed

Binary file test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png has changed

Binary file test-data/pl.rank_genes_groups_violin.Ery.png has changed

Binary file test-data/pl.rank_genes_groups_violin.Mk.png has changed

Binary file test-data/pl.rank_genes_groups_violin.Mo.png has changed

Binary file test-data/pl.rank_genes_groups_violin.Neu.png has changed

Binary file test-data/pl.rank_genes_groups_violin.progenitor.png has changed

Binary file test-data/pl.scatter.krumsiek11.png has changed

Binary file test-data/pl.scatter.pbmc68k_reduced.png has changed

Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed

Binary file test-data/pl.stacked_violin.krumsiek11.png has changed

Binary file test-data/pl.tsne.krumsiek11.png has changed

Binary file test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png has changed

Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed

Binary file test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad has changed

Binary file test-data/pp.combat.blobs.h5ad has changed

Binary file test-data/pp.downsample_counts.random-randint.h5ad has changed

Binary file test-data/pp.filter_cells.krumsiek11-max_genes.h5ad has changed

Binary file test-data/pp.filter_cells.krumsiek11-min_counts.h5ad has changed

Binary file test-data/pp.filter_genes.krumsiek11-min_counts.h5ad has changed

Binary file test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad has changed

Binary file test-data/pp.highly_variable_genes.seurat.blobs.h5ad has changed

Binary file test-data/pp.log1p.krumsiek11.h5ad has changed

Binary file test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/pp.normalize_total.krumsiek11.h5ad has changed

Binary file test-data/pp.pca.krumsiek11.h5ad has changed

Binary file test-data/pp.pca.krumsiek11_chunk.h5ad has changed

Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed

Binary file test-data/pp.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad has changed

Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed

Binary file test-data/pp.regress_out.krumsiek11.h5ad has changed

Binary file test-data/pp.scale.krumsiek11.h5ad has changed

Binary file test-data/pp.scale_max_value.krumsiek11.h5ad has changed

Binary file test-data/pp.sqrt.krumsiek11.h5ad has changed

Binary file test-data/pp.subsample.krumsiek11_fraction.h5ad has changed

Binary file test-data/pp.subsample.krumsiek11_n_obs.h5ad has changed

Binary file test-data/sparce_csr_matrix.h5ad has changed

Binary file test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad has changed

Binary file test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.paga.neighbors.paul15_gauss_braycurtis.h5ad has changed

Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

Binary file test-data/tl.pca.krumsiek11.h5ad has changed

Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed

Binary file test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad has changed

Binary file test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad has changed

Binary file test-data/tl.score_genes.krumsiek11.h5ad has changed

Binary file test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad has changed

Binary file test-data/tl.tsne.krumsiek11.h5ad has changed

Binary file test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed