changeset 12:9740d430d9f3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author iuc
date Wed, 31 Jul 2024 18:05:14 +0000
parents 336f7f889475
children 450363fe2881
files cluster_reduce_dimension.xml macros.xml test-data/blobs.h5ad test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad test-data/external.pp.magic.all_genes.krumsiek11.h5ad test-data/external.pp.magic.pca_only.krumsiek11.h5ad test-data/krumsiek11.h5ad test-data/pbmc68k_reduced.h5ad test-data/pl.clustermap.krumsiek11.png test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.dotplot.krumsiek11.png test-data/pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.draw_graph.png test-data/pl.embedding_density.pbmc68k_reduced.png test-data/pl.heatmap.krumsiek11.png test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png test-data/pl.highly_variable_genes.seurat.blobs.png test-data/pl.matrixplot.krumsiek11.png test-data/pl.paga.paul15_gauss_braycurtis.png test-data/pl.paga_compare.paul15_gauss_braycurtis.png test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf test-data/pl.pca_loadings.pp.pca.krumsiek11.png test-data/pl.pca_overview.pp.pca.krumsiek11.png test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_violin.Ery.png test-data/pl.rank_genes_groups_violin.Mk.png test-data/pl.rank_genes_groups_violin.Mo.png test-data/pl.rank_genes_groups_violin.Neu.png test-data/pl.rank_genes_groups_violin.progenitor.png test-data/pl.scatter.krumsiek11.png test-data/pl.scatter.pbmc68k_reduced.png test-data/pl.scatter.umap.pbmc68k_reduced.png test-data/pl.stacked_violin.krumsiek11.png test-data/pl.tsne.krumsiek11.png test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png test-data/pl.violin.pbmc68k_reduced_custom.png test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad test-data/pp.combat.blobs.h5ad test-data/pp.downsample_counts.random-randint.h5ad test-data/pp.filter_cells.krumsiek11-max_genes.h5ad test-data/pp.filter_cells.krumsiek11-min_counts.h5ad test-data/pp.filter_genes.krumsiek11-min_counts.h5ad test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad test-data/pp.highly_variable_genes.seurat.blobs.h5ad test-data/pp.log1p.krumsiek11.h5ad test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.normalize_total.krumsiek11.h5ad test-data/pp.pca.krumsiek11.h5ad test-data/pp.pca.krumsiek11_chunk.h5ad test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad test-data/pp.recipe_zheng17.random-randint.h5ad test-data/pp.regress_out.krumsiek11.h5ad test-data/pp.scale.krumsiek11.h5ad test-data/pp.scale_max_value.krumsiek11.h5ad test-data/pp.sqrt.krumsiek11.h5ad test-data/pp.subsample.krumsiek11_fraction.h5ad test-data/pp.subsample.krumsiek11_n_obs.h5ad test-data/sparce_csr_matrix.h5ad test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.paga.neighbors.paul15_gauss_braycurtis.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.pca.krumsiek11.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad test-data/tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv test-data/tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad test-data/tl.score_genes.krumsiek11.h5ad test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad test-data/tl.tsne.krumsiek11.h5ad test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad
diffstat 86 files changed, 226 insertions(+), 134 deletions(-) [+]
line wrap: on
line diff
--- a/cluster_reduce_dimension.xml	Wed Sep 22 21:02:36 2021 +0000
+++ b/cluster_reduce_dimension.xml	Wed Jul 31 18:05:14 2024 +0000
@@ -1,6 +1,5 @@
-<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description>with scanpy</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
         <xml name="pca_inputs">
@@ -20,7 +19,7 @@
                     <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
                         label="Compute standard PCA from covariance matrix?"
                         help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>
-                    <expand macro="svd_solver"/> 
+                    <expand macro="svd_solver"/>
                     <param argument="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
                 </when>
             </conditional>
@@ -61,8 +60,8 @@
     use_highly_variable=$method.use_highly_variable
 ]]></token>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="0.7.0">louvain</requirement>
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -111,7 +110,7 @@
 #else if $method.method == 'tl.tsne'
 sc.tl.tsne(
     adata=adata,
-    #if $method.n_pcs
+    #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
     perplexity=$method.perplexity,
@@ -127,7 +126,7 @@
     min_dist=$method.min_dist,
     spread=$method.spread,
     n_components=$method.n_components,
-    #if $method.maxiter
+    #if str($method.maxiter) != ''
     maxiter=$method.maxiter,
     #end if
     alpha=$method.alpha,
@@ -138,7 +137,6 @@
     copy=False)
 
 #else if $method.method == 'tl.draw_graph'
-
     #if str($method.adjacency) != 'None'
 from scipy import io
 adjacency = io.mmread('$method.adjacency')
@@ -147,18 +145,18 @@
 sc.tl.draw_graph(
     adata=adata,
     layout='$method.layout',
-#if str($method.root) != ''
+#if $method.root
     #set $root=([int(x.strip()) for x in str($method.root).split(',')])
     root=$root,
 #end if
     random_state=$method.random_state,
-    #if str($method.init_pos) != ''
+    #if $method.init_pos
     init_pos='$method.init_pos',
     #end if
     #if str($method.adjacency) != 'None'
     adjacency=adjacency,
     #end if
-    #if str($method.key_ext) != ''
+    #if $method.key_ext
     key_ext='$method.key_ext',
     #end if
     copy=False)
@@ -179,6 +177,19 @@
     min_group_size=$method.min_group_size,
     allow_kendall_tau_shift=$method.allow_kendall_tau_shift,
     copy=False)
+
+#else if $method.method == "tl.embedding_density"
+sc.tl.embedding_density(
+    adata=adata,
+    basis='$method.basis',
+#if $method.groupby
+    groupby='$method.groupby',
+#end if
+#if $method.key_added
+    key_added='$method.key_added',
+#end if
+    )
+
 #end if
 
 @CMD_anndata_write_outputs@
@@ -198,6 +209,7 @@
                 <option value="tl.draw_graph">Force-directed graph drawing, using 'tl.draw_graph'</option>
                 <option value="tl.dpt">Infer progression of cells through geodesic distance along the graph, using 'tl.dpt'</option>
                 <option value="tl.paga">Generate cellular maps of differentiation manifolds with complex topologies, using 'tl.paga'</option>
+                <option value="tl.embedding_density">Calculate the density of cells in an embedding (per condition)</option>
             </param>
             <when value="tl.louvain">
                 <conditional name="flavor">
@@ -282,21 +294,32 @@
                 <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs').">
                     <expand macro="sanitize_query" />
                 </param>
-                <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/>
+                <param argument="use_rna_velocity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/>
                 <param argument="model" type="select" label="PAGA connectivity model" help="">
                     <option value="v1.2">v1.2</option>
                     <option value="v1.0">v1.0</option>
                 </param>
             </when>
-        </conditional>            
+            <when value="tl.embedding_density">
+                <param argument="basis" type="text" value="umap" label="The embedding over which the density will be calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="groupby" type="text" optional="true" value="" label="Key for categorical observation/cell annotation for which densities are calculated per category." >
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="key_added" type="text" optional="true" value="" label="Name of the .obs covariate that will be added with the density estimates.">
+                    <expand macro="sanitize_query" />
+                </param>
+            </when>
+        </conditional>
         <expand macro="inputs_common_advanced"/>
     </inputs>
     <outputs>
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
-            <!-- test 0 -->
+        <test expect_num_outputs="2">
+            <!-- test 1 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.louvain"/>
@@ -326,8 +349,8 @@
             </output>
             <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 1 -->
+        <test expect_num_outputs="2">
+            <!-- test 2 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.leiden"/>
@@ -352,8 +375,8 @@
             </output>
             <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 1 -->
+        <test expect_num_outputs="2">
+            <!-- test 3 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.pca"/>
@@ -384,8 +407,8 @@
             </output>
             <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
         </test>
-        <!--<test>
-            < test 3 >
+        <test expect_num_outputs="2">
+            <!-- test 4 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.pca"/>
@@ -397,21 +420,24 @@
                 </conditional>
                 <param name="use_highly_variable" value="false"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.pca"/>
-                <has_text_matching expression="data=adata"/>
-                <has_text_matching expression="n_comps=20"/>
-                <has_text_matching expression="dtype='float32'"/>
-                <has_text_matching expression="copy=False"/>
-                <has_text_matching expression="chunked=True"/>
-                <has_text_matching expression="chunk_size=50"/>
-                <has_text_matching expression="use_highly_variable=False"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.pp.pca"/>
+                    <has_text_matching expression="data=adata"/>
+                    <has_text_matching expression="dtype='float32'"/>
+                    <has_text_matching expression="copy=False"/>
+                    <has_text_matching expression="chunked=True"/>
+                    <has_text_matching expression="chunk_size=50"/>
+                    <has_text_matching expression="use_highly_variable=False"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        -->
-        <test>
-            <!-- test 2 -->
+        <test expect_num_outputs="2">
+            <!-- test 5 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.pca"/>
@@ -441,8 +467,8 @@
             </output>
             <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
         </test>
-        <test>
-            <!-- test 3 -->
+        <test expect_num_outputs="2">
+            <!-- test 6 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.diffmap"/>
@@ -458,8 +484,8 @@
             </output>
             <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 4 -->
+        <test expect_num_outputs="2">
+            <!-- test 7 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.tsne"/>
@@ -486,8 +512,8 @@
             </output>
             <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 5 -->
+        <test expect_num_outputs="2">
+            <!-- test 8 -->
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.umap"/>
@@ -524,8 +550,8 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <!-- test 6 -->
+        <test expect_num_outputs="2">
+            <!-- test 9 -->
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.draw_graph"/>
@@ -544,8 +570,8 @@
             </output>
             <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 7 -->
+        <test expect_num_outputs="2">
+            <!-- test 10 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.paga"/>
@@ -566,8 +592,8 @@
             </output>
             <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 8 -->
+        <test expect_num_outputs="2">
+            <!-- test 11 -->
             <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.dpt"/>
@@ -590,6 +616,26 @@
             </output>
             <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
+        <test expect_num_outputs="2">
+            <!-- test 12 -->
+            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
+            <conditional name="method">
+                <param name="method" value="tl.embedding_density"/>
+                <param name="basis" value="umap"/>
+                <param name="key_added" value="umap_density"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.embedding_density"/>
+                    <has_text_matching expression="basis='umap'"/>
+                    <has_text_matching expression="key_added='umap_density'"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" file="tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 Cluster cells into subgroups (`tl.louvain`)
@@ -602,7 +648,7 @@
 This requires to run `pp.neighbors`, first.
 
 More details on the `tl.louvain scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.louvain.html>`_
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.louvain.html>`_
 
 Cluster cells into subgroups (`tl.leiden`)
 ==========================================
@@ -612,7 +658,7 @@
 The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015.
 
 More details on the `tl.leiden scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.leiden.html>`_
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.leiden.html>`_
 
 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`
 ============================================================================================================
@@ -620,7 +666,7 @@
 @CMD_pca_outputs@
 
 More details on the `pp.pca scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.pca.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.pca.html>`__
 
 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`
 ============================================================================================================
@@ -628,7 +674,7 @@
 @CMD_pca_outputs@
 
 More details on the `tl.pca scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.pca.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.pca.html>`__
 
 Diffusion Maps, using `tl.diffmap`
 ==================================
@@ -645,24 +691,24 @@
 `method=='umap'`. Differences between these options shouldn't usually be
 dramatic.
 
-The diffusion map representation of data are added to the return AnnData in the multi-dimensional 
-observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors 
+The diffusion map representation of data are added to the return AnnData in the multi-dimensional
+observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors
 as colum. It can be accessed using the inspect tool for AnnData
 
 More details on the `tl.diffmap scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.diffmap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.diffmap.html>`__
 
 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`
 =======================================================================
 
 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been
 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,
-we use the implementation of *scikit-learn* (Pedregosa et al, 2011). 
+we use the implementation of *scikit-learn* (Pedregosa et al, 2011).
 
 It returns `X_tsne`, tSNE coordinates of data.
 
 More details on the `tl.tsne scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.tsne.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.tsne.html>`__
 
 Embed the neighborhood graph using UMAP, using `tl.umap`
 ========================================================
@@ -678,30 +724,30 @@
 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint
 <https://doi.org/10.1101/298430>`__.
 
-The UMAP coordinates of data are added to the return AnnData in the multi-dimensional 
+The UMAP coordinates of data are added to the return AnnData in the multi-dimensional
 observations annotation (obsm). This data is accessible using the inspect tool for AnnData
 
 More details on the `tl.umap scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.umap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.umap.html>`__
 
 Force-directed graph drawing, using `tl.draw_graph`
 ===================================================
 
-Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs. 
-It has been suggested for visualizing single-cell data by Islam et al, 11. 
-Many other layouts as implemented in igraph are available. Similar approaches have been used by 
+Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs.
+It has been suggested for visualizing single-cell data by Islam et al, 11.
+Many other layouts as implemented in igraph are available. Similar approaches have been used by
 Zunder et al, 2015 or Weinreb et al, 2016.
 
-This is an alternative to tSNE that often preserves the topology of the data better. 
+This is an alternative to tSNE that often preserves the topology of the data better.
 This requires to run `pp.neighbors`, first.
 
 The default layout (ForceAtlas2) uses the package fa2.
 
-The coordinates of graph layout are added to the return AnnData in the multi-dimensional 
+The coordinates of graph layout are added to the return AnnData in the multi-dimensional
 observations annotation (obsm). This data is accessible using the inspect tool for AnnData.
 
 More details on the `tl.draw_graph scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.draw_graph.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.draw_graph.html>`__
 
 Infer progression of cells through geodesic distance along the graph (`tl.dpt`)
 ===============================================================================
@@ -714,7 +760,7 @@
 `n_branchings>1`. We recommend, however, to only use
 `tl.dpt` for computing pseudotime (`n_branchings=0`) and
 to detect branchings via `paga`. For pseudotime, you need
-to annotate your data with a root cell. 
+to annotate your data with a root cell.
 
 This requires to run `pp.neighbors`, first. In order to
 reproduce the original implementation of DPT, use `method=='gauss'` in
@@ -730,7 +776,7 @@
 The tool is similar to the R package `destiny` of Angerer et al (2016).
 
 More details on the `tl.dpt scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.dpt.html>`_
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.dpt.html>`_
 
 
 Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`)
@@ -761,7 +807,7 @@
 These datasets are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
 
 More details on the `tl.paga scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.paga.html>`_
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.paga.html>`_
     ]]></help>
     <expand macro="citations"/>
 </tool>
--- a/macros.xml	Wed Sep 22 21:02:36 2021 +0000
+++ b/macros.xml	Wed Jul 31 18:05:14 2024 +0000
@@ -1,12 +1,17 @@
 <macros>
-    <token name="@version@">1.7.1</token>
-    <token name="@profile@">19.01</token>
-    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
+    <token name="@TOOL_VERSION@">1.9.6</token>
+    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@profile@">21.09</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="@TOOL_VERSION@">scanpy</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>
+            <requirement type="package" version="3.0.0">magic-impute</requirement>
             <yield />
         </requirements>
     </xml>
@@ -15,9 +20,15 @@
             <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 +67,7 @@
         <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 +77,12 @@
     </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)
 ]]>
@@ -414,6 +425,7 @@
             <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
                 <option value="all">All variables in 'adata.var_names'</option>
                 <option value="custom">Subset of variables in 'adata.var_names'</option>
+                <option value="customfile">Subset of variables as a tabular file</option>
             </param>
             <when value="all"/>
             <when value="custom">
@@ -421,6 +433,9 @@
                     <expand macro="sanitize_query" />
                 </param>
             </when>
+            <when value="customfile">
+                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
+            </when>
         </conditional>
     </xml>
     <xml name="param_num_categories">
@@ -457,15 +472,17 @@
         <expand macro="param_num_categories"/>
     </xml>
     <token name="@CMD_params_inputs@"><![CDATA[
-    #if $method.var_names.type == 'all'
-    var_names=adata.var_names,
-#else
+    #if $method.var_names.type == 'custom'
     #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
     var_names=$var_names,
-#end if
-#if str($method.groupby) != ''
+    #else if $method.var_names.type == 'customfile'
+    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
+    #else
+    var_names=adata.var_names,
+    #end if
+    #if $method.groupby
     groupby='$method.groupby',
-#end if
+    #end if
     num_categories=$method.num_categories,
     ]]></token>
     <xml name="params_plots">
@@ -491,15 +508,15 @@
     var_group_positions=$var_group_positions,
     var_group_labels=$var_group_labels,
     #end if
-#if $method.var_group_rotation
-    var_group_rotation=$method.var_group_rotation,
-#end if
-#if $method.figsize.test == 'yes'
-    figsize=($method.figsize.width, $method.figsize.height),
-#end if
-#if $method.layer != ''
-    layer='$method.layer',
-#end if
+    #if str($method.var_group_rotation) != ''
+        var_group_rotation=$method.var_group_rotation,
+    #end if
+    #if $method.figsize.test == 'yes'
+        figsize=($method.figsize.width, $method.figsize.height),
+    #end if
+    #if $method.layer
+        layer='$method.layer',
+    #end if
     ]]></token>
     <xml name="matplotlib_color">
         <option value="AliceBlue">AliceBlue</option>
@@ -652,9 +669,8 @@
         <option value="YellowGreen">YellowGreen</option>
     </xml>
     <xml name="param_matplotlib_pyplot_edgecolors">
-        <param argument="edgecolors" type="select" label="Edge color of the marker" help="">
+        <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
             <option value="face">The edge color will always be the same as the face color</option>
-            <option value="none">No patch boundary will be drawn</option>
             <expand macro="matplotlib_color"/>
         </param>
     </xml>
@@ -692,17 +708,19 @@
         </section>
     </xml>
     <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
-    #if $method.matplotlib_pyplot_scatter.vmin
+    #if str($method.matplotlib_pyplot_scatter.vmin) != ''
     vmin=$method.matplotlib_pyplot_scatter.vmin,
     #end if
-    #if $method.matplotlib_pyplot_scatter.vmax
+    #if str($method.matplotlib_pyplot_scatter.vmax) != ''
     vmax=$method.matplotlib_pyplot_scatter.vmax,
     #end if
-    #if $method.matplotlib_pyplot_scatter.alpha
+    #if str($method.matplotlib_pyplot_scatter.alpha) != ''
     alpha=$method.matplotlib_pyplot_scatter.alpha,
     #end if
-    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
-    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
+    lw=$method.matplotlib_pyplot_scatter.linewidths,
+    #if $method.matplotlib_pyplot_scatter.edgecolors
+    ec='$method.matplotlib_pyplot_scatter.edgecolors'
+    #end if
     ]]></token>
     <xml name="conditional_stripplot">
         <conditional name="stripplot">
@@ -742,13 +760,7 @@
         </param>
     </xml>
     <token name="@CMD_params_violin_plots@"><![CDATA[
-    stripplot=$method.violin_plot.stripplot.stripplot,
-#if $method.violin_plot.stripplot.stripplot == "True"
-    jitter=$method.violin_plot.stripplot.jitter.jitter,
-    #if $method.violin_plot.stripplot.jitter.jitter == "True"
-    size=$method.violin_plot.stripplot.jitter.size,
-    #end if
-#end if
+    @CMD_conditional_stripplot@
     multi_panel=$method.violin_plot.multi_panel.multi_panel,
 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
     figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
@@ -766,7 +778,7 @@
                 <option value="h">horizontal</option>
             </param>
             <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
-            <param argument="color" type="select" label="Color for all of the elements" help="">
+            <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
                 <expand macro="matplotlib_color"/>
             </param>
             <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
@@ -778,7 +790,9 @@
     orient='$method.seaborn_violinplot.orient',
 #end if
     linewidth=$method.seaborn_violinplot.linewidth,
+    #if $method.seaborn_violinplot.color
     color='$method.seaborn_violinplot.color',
+    #end if
     saturation=$method.seaborn_violinplot.saturation
     ]]></token>
     <xml name="param_color">
@@ -787,7 +801,7 @@
         </param>
     </xml>
     <token name="@CMD_param_color@"><![CDATA[
-#if str($method.color) != ''
+#if $method.color
     #set $color = ([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
@@ -798,7 +812,7 @@
         </param>
     </xml>
     <token name="@CMD_params_groups@"><![CDATA[
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
@@ -868,14 +882,12 @@
         </param>
     </xml>
     <xml name="param_palette">
-        <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help="">
-            <option value="default">Default</option>
+        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
     <xml name="param_color_map">
-        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
-            <option value="None">Default</option>
+        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -931,7 +943,7 @@
             </param>
             <when value="True">
                 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
-                <param argument="edges_color" type="select" label="Color of edges">
+                <param argument="edges_color" type="select" optional="true" label="Color of edges">
                     <expand macro="matplotlib_color"/>
                 </param>
             </when>
@@ -942,7 +954,9 @@
 #if str($method.edges.edges) == 'True'
     edges=True,
     edges_width=$method.edges.edges_width,
+    #if $method.edges.edges_color
     edges_color='$method.edges.edges_color',
+    #end if
 #else
     edges=False,
 #end if
@@ -952,7 +966,7 @@
         <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
     </xml>
     <xml name="param_cmap">
-        <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
+        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -979,10 +993,10 @@
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
     @CMD_param_size@
-    #if str($method.plot.color_map) != 'None'
+    #if $method.plot.color_map
     color_map='$method.plot.color_map',
     #end if
-    #if str($method.plot.palette) != ''
+    #if $method.plot.palette
     palette='$method.plot.palette',
     #end if
     frameon=$method.plot.frameon,
@@ -1052,18 +1066,18 @@
     </xml>
     <token name="@CMD_params_pl_paga@"><![CDATA[
     threshold=$method.threshold,
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
-#if str($method.color) != ''
+#if $method.color
     #set $color=([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
 #if $method.pos
     pos=np.fromfile($method.pos, dtype=dt),
 #end if
-#if str($method.labels) != ''
+#if $method.labels
     #set $labels=([x.strip() for x in str($method.labels).split(',')])
     labels=$labels,
 #end if
@@ -1072,7 +1086,7 @@
     init_pos=np.fromfile($method.init_pos, dtype=dt),
 #end if
     random_state=$method.random_state,
-#if str($method.root) != ''
+#if $method.root
     #set $root=([int(x.strip()) for x in str($method.root).split(',')])
     root=$root,
 #end if
@@ -1088,15 +1102,17 @@
     node_size_scale=$method.node_size_scale,
     node_size_power=$method.node_size_power,
     edge_width_scale=$method.edge_width_scale,
-#if $method.min_edge_width
+#if str($method.min_edge_width) != ''
     min_edge_width=$method.min_edge_width,
 #end if
-#if $method.max_edge_width
+#if str($method.max_edge_width) != ''
     max_edge_width=$method.max_edge_width,
 #end if
     arrowsize=$method.arrowsize,
     normalize_to_color=$method.normalize_to_color,
+    #if $method.cmap
     cmap='$method.cmap',
+    #end if
 #if $method.title
     title='$method.title',
 #end if
@@ -1112,10 +1128,10 @@
         </param>
     </xml>
     <xml name="param_n_genes">
-        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
+        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
     </xml>
     <xml name="pl_dotplot">
-        <param argument="color_map" type="select" label="Color palette">
+        <param argument="color_map" type="select" optional="true" label="Color palette">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
         <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
@@ -1123,7 +1139,9 @@
         <expand macro="section_matplotlib_pyplot_scatter"/>
     </xml>
     <token name="@CMD_pl_dotplot@"><![CDATA[
+    #if $method.color_map
     color_map='$method.color_map',
+    #end if
     #if str($method.dot_max) != ''
     dot_max=$method.dot_max,
     #end if
@@ -1174,17 +1192,19 @@
     <token name="@CMD_pl_heatmap@"><![CDATA[
     swap_axes=$method.swap_axes,
     show_gene_labels=$method.show_gene_labels,
+    #if $method.matplotlib_pyplot_imshow.cmap
     cmap='$method.matplotlib_pyplot_imshow.cmap',
+    #end if
     #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
     interpolation='$method.matplotlib_pyplot_imshow.interpolation',
     #end if
-    #if $method.matplotlib_pyplot_imshow.alpha
+    #if str($method.matplotlib_pyplot_imshow.alpha) != ''
     alpha=$method.matplotlib_pyplot_imshow.alpha,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmin
+    #if str($method.matplotlib_pyplot_imshow.vmin) != ''
     vmin=$method.matplotlib_pyplot_imshow.vmin,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmax
+    #if str($method.matplotlib_pyplot_imshow.vmax) != ''
     vmax=$method.matplotlib_pyplot_imshow.vmax,
     #end if
     origin='$method.matplotlib_pyplot_imshow.origin'
@@ -1197,10 +1217,8 @@
     </xml>
     <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
     @CMD_params_groups@
-    #if str($method.n_genes) != ''
     n_genes=$method.n_genes,
-    #end if
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     ]]>
@@ -1208,7 +1226,7 @@
     <xml name="pl_matrixplot">
         <expand macro="param_swap_axes"/>
         <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
-            <param argument="cmap" type="select" label="Color palette">
+            <param argument="cmap" type="select" optional="true" label="Color palette">
                 <expand macro="seaborn_color_palette_options"/>
             </param>
             <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
@@ -1220,15 +1238,19 @@
     </xml>
     <token name="@CMD_pl_matrixplot@"><![CDATA[
     swap_axes=$method.swap_axes,
+    #if $method.matplotlib_pyplot_pcolor.cmap
     cmap='$method.matplotlib_pyplot_pcolor.cmap',
-    #if $method.matplotlib_pyplot_pcolor.vmin
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
     vmin=$method.matplotlib_pyplot_pcolor.vmin,
     #end if
-    #if $method.matplotlib_pyplot_pcolor.vmax
+    #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
     vmax=$method.matplotlib_pyplot_pcolor.vmax,
     #end if
-    edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
-    #if $method.matplotlib_pyplot_pcolor.alpha
+    #if $method.matplotlib_pyplot_pcolor.edgecolors
+    ec='$method.matplotlib_pyplot_pcolor.edgecolors',
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
     alpha=$method.matplotlib_pyplot_pcolor.alpha,
     #end if
     snap=$method.matplotlib_pyplot_pcolor.snap
@@ -1240,7 +1262,7 @@
             <expand macro="conditional_stripplot"/>
             <expand macro="param_scale"/>
         </section>
-        <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
+        <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
             <option value="muted">muted</option>
             <expand macro="seaborn_color_palette_options"/>
         </param>
@@ -1255,7 +1277,9 @@
     swap_axes=$method.swap_axes,
     @CMD_conditional_stripplot@
     scale='$method.violin_plot.scale',
+    #if $method.row_palette
     row_palette='$method.row_palette',
+    #end if
     #if str($method.standard_scale) != 'None'
     standard_scale='$method.standard_scale',
     #end if
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv	Wed Jul 31 18:05:14 2024 +0000
@@ -0,0 +1,11 @@
+	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49
+CD14+ Monocyte	PILRA	PSAP	CD68	TMEM176B	FTL	NPC2	LST1	FCGR3A	FCER1G	CEBPB	FCN1	SERPINA1	OAZ1	CFD	FTH1	HCK	AIF1	SAT1	CTSS	S100A11	MS4A7	TYROBP	COTL1	STXBP2	RP11-290F20.3	S100A4	IFITM2	SPI1	DUSP1	SESN2	IFITM3	MPP1	GALE	CORO1B	RP11-390E23.6	VIMP	RSBN1L-AS1	CHD4	CFP	GSTP1	PFN1	FCGRT	ADTRP	ARHGDIB	AMICA1	HLA-DRB5	CST3	GRN	HLA-DPA1	SSR3
+CD19+ B	TNFRSF13B	CD79B	SMARCB1	PNOC	CCDC50	AL928768.3	BANK1	MS4A1	CD79A	ISG20	IGLL5	TNFRSF17	KIAA0125	TPD52	PEBP1	FKBP11	CCDC132	SUB1	POU2AF1	MZB1	PTPRCAP	UBE2J1	BLK	SPIB	DERL3	FAM63B	MPHOSPH9	IGJ	FCRLA	XBP1	NCF1	SSR3	CD52	TSHZ2	PDLIM1	VIMP	SSR4	S1PR4	SELL	HMGA1	NUCB2	JUN	CD27	ARHGDIB	GYPC	CALR	ADTRP	BTG1	EXOG	RARRES3
+CD34+	PRSS57	C19orf77	SPINK2	RP11-620J15.3	SNHG7	CYTL1	EGFL7	NGFRAP1	SOX4	NFE2	EGR1	RP3-467N11.1	H1FX	CDK6	SERPINB1	SPINT2	HMGA1	IL1B	NUCB2	RPLP0	IGFBP7	RPLP1	ATXN7L3B	RPS3	C1orf228	KIAA0125	RPL3	SYPL1	CD63	LDHB	SEPT1	JUN	FAM101B	PRKCQ-AS1	MATK	PEBP1	SELL	ITM2A	SSR3	SPON2	XBP1	UBE2J1	VIMP	GYPC	STK17A	STMN1	VIM	MZB1	HOPX	CD99
+CD4+/CD25 T Reg	IL32	SPOCK2	ACTG1	CD2	CD3D	GPR171	ARHGDIB	ACOX1	MAL	SIT1	GIMAP4	AES	CD52	SEPT1	TMSB10	LAT	STMN1	LINC00402	CD27	TSHZ2	S1PR4	CD3E	PFN1	CD99	AQP3	PTPRCAP	CD3G	LY9	LCK	CD247	S100A4	CCR7	TTC39C	CORO1B	MPHOSPH9	FYB	RPSA	FLT3LG	B2M	GIMAP7	PRKCQ-AS1	SELL	BTG1	CCDC132	GYPC	DENND2D	LDHB	IL7R	ITM2A	RPLP0
+CD4+/CD45RA+/CD25- Naive T	EAF2	GNG7	SSR4	CALR	DERL3	MANF	IGJ	XBP1	ATXN7L3B	SSR3	UBE2J1	CD79A	MZB1	RP3-467N11.1	TNFRSF17	NCF1	CDK6	SUB1	POU2AF1	AL928768.3	FKBP11	VIMP	GYPC	JUN	CD27	PEBP1	SMARCB1	FLT3LG	RPLP1	RPLP0	CCDC50	ISG20	IGLL5	HCST	GSTP1	GPX1	CD52	VIM	PTPRCAP	FCGRT	CD74	B2M	RPL3	CYTL1	SPINK2	PRSS57	C19orf77	RP11-620J15.3	FAM101B	CCDC132
+CD4+/CD45RO+ Memory	RNF138	NOSIP	IFITM1	LCK	RARRES3	ALOX5AP	FAM63B	RAB3IP	GZMK	CD3G	SEPT1	LDHB	SELL	CD3D	EXOG	RPSA	CD247	AES	CD52	TMSB10	NUCB2	DENND2D	RPL3	RPLP1	ACTG1	FYB	GIMAP7	CORO1B	LY9	CD7	PFN1	RPS3	GYPC	CD2	ARHGDIB	IL32	RPLP0	CD99	CD3E	GIMAP4	HCST	B2M	LAT	ISG20	ITM2A	FKBP11	SERPINB1	STK17A	CCR7	PTPRCAP
+CD56+ NK	CST7	SPON2	HOPX	GNLY	NKG7	CTSW	KLRC2	CD7	MATK	PCIF1	CLIC3	FGFBP2	SYPL1	GZMB	C9orf142	PRF1	CD247	HCST	GZMA	GZMH	STMN1	ALOX5AP	CD63	CD99	IGFBP7	GZMM	CCL5	B2M	DENND2D	GIMAP7	RARRES3	SIT1	IFITM1	PFN1	EXOG	XBP1	IFITM2	GIMAP4	VIMP	STK17A	LCK	GZMK	SEPT1	SSR3	CD8A	CD3G	SPOCK2	RPS3	LDHB	IL32
+CD8+ Cytotoxic T	FAM101B	ADTRP	GZMK	HCST	LAT	EGR1	CD8B	CCL5	RPL3	LINC00402	FGFBP2	GZMM	RPS3	CD3E	GYPC	DENND2D	C9orf142	GZMA	SEPT1	JUN	FYB	CD8A	SELL	ALOX5AP	CD3G	STK17A	AQP3	C1orf228	CD3D	HOPX	NKG7	CD2	NGFRAP1	RPLP1	RPSA	CCR7	IL7R	SPON2	PRF1	RARRES3	PRKCQ-AS1	FKBP11	MANF	CTSW	GNLY	CD27	LDHB	MAL	LTB	RPLP0
+CD8+/CD45RA+ Naive Cytotoxic	RP11-291B21.2	CD8A	CD8B	RSBN1L-AS1	GIMAP5	GZMM	GALE	CCR7	STK17A	RAB3IP	GZMH	GIMAP7	CD3E	C1orf228	LCK	CCL5	PEBP1	CD27	GYPC	LDHB	RNF34	CD99	CD3G	PFN1	IL7R	CD2	C9orf142	TMSB10	NGFRAP1	S1PR4	ITM2A	CD7	RPS3	IL32	FYB	IFITM1	CD52	LAT	GIMAP4	MAL	STMN1	NOSIP	RARRES3	SPOCK2	ACTG1	PRF1	CD3D	RPLP1	SELL	GZMA
+Dendritic	HLA-DQB1	CST3	HLA-DRB1	HLA-DQA2	HLA-DQA1	LYZ	HLA-DPB1	HLA-DPA1	HLA-DMA	HLA-DRA	VIM	CD74	ALDH2	FCER1A	GPX1	HLA-DRB5	LGALS2	MNDA	FCGRT	GRN	HLA-DMB	FOS	CPVL	CLEC10A	AMICA1	CFP	LY86	GSTP1	RP11-473M20.7	IL1B	GSN	SPINT2	CCDC163P	IGFBP7	EXOG	DUSP1	CD63	COTL1	FTH1	SPI1	TYROBP	SPIB	S100A11	OAZ1	CTSS	CCDC50	AIF1	SERPINB1	TMSB10	PCIF1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv	Wed Jul 31 18:05:14 2024 +0000
@@ -0,0 +1,11 @@
+	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33
+CD14+ Monocyte	PILRA	PSAP	CD68	TMEM176B	FTL	NPC2	LST1	FCGR3A	FCER1G	CEBPB	FCN1	SERPINA1	OAZ1	CFD	FTH1	HCK	AIF1	SAT1	CTSS	S100A11	TYROBP	COTL1	S100A4	SPI1	DUSP1									
+CD19+ B	TNFRSF13B	CD79B	SMARCB1	PNOC	CCDC50	AL928768.3	BANK1	MS4A1	CD79A	ISG20	IGLL5	TNFRSF17	KIAA0125	TPD52	PEBP1	FKBP11	SUB1	POU2AF1	MZB1	PTPRCAP	DERL3	XBP1	CD52											
+CD34+	PRSS57	C19orf77	SPINK2	RP11-620J15.3	SNHG7	CYTL1	EGFL7	NGFRAP1	SOX4	NFE2	EGR1	RP3-467N11.1	H1FX	CDK6	SERPINB1	SPINT2	HMGA1	IL1B	NUCB2	RPLP0	IGFBP7	RPLP1	ATXN7L3B	RPS3	KIAA0125	RPL3	SYPL1	LDHB	SEPT1	FAM101B				
+CD4+/CD25 T Reg	IL32	SPOCK2	ACTG1	CD2	CD3D	ARHGDIB	GIMAP4	AES	CD52	SEPT1	TMSB10	LAT	STMN1	CD27	CD3E	PFN1	CD99	PTPRCAP	CD3G	LCK	CD247													
+CD4+/CD45RA+/CD25- Naive T																																		
+CD4+/CD45RO+ Memory	RNF138	NOSIP	IFITM1	LCK	RARRES3	ALOX5AP	RAB3IP	GZMK	CD3G	SEPT1	LDHB	SELL	CD3D	EXOG	RPSA	CD247	AES	CD52	TMSB10	RPL3														
+CD56+ NK	CST7	SPON2	HOPX	GNLY	NKG7	CTSW	KLRC2	CD7	MATK	PCIF1	CLIC3	FGFBP2	SYPL1	GZMB	C9orf142	PRF1	CD247	HCST	GZMA	GZMH	STMN1	ALOX5AP	CD63	CD99	IGFBP7	GZMM	CCL5	B2M	DENND2D	GIMAP7	RARRES3	SIT1	PFN1	XBP1
+CD8+ Cytotoxic T	FAM101B	ADTRP	GZMK	HCST	LAT	EGR1	CD8B	CCL5	RPL3	LINC00402	FGFBP2	GZMM	RPS3	CD3E	GYPC	C9orf142	SEPT1	SELL	CD3G	CD3D	HOPX	NGFRAP1												
+CD8+/CD45RA+ Naive Cytotoxic	RP11-291B21.2	CD8A	CD8B	RSBN1L-AS1	GIMAP5	GZMM	GALE	CCR7	STK17A	RAB3IP	GIMAP7	CD3E	LCK	PEBP1	CD27	LDHB	CD99	CD3G	C9orf142	NGFRAP1	IL32													
+Dendritic	HLA-DQB1	CST3	HLA-DRB1	HLA-DQA2	HLA-DQA1	HLA-DPB1	HLA-DPA1	HLA-DRA	CD74																									
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