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changeset 11:2d02d9702d3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
author iuc
date Wed, 08 Nov 2023 14:44:39 +0000
parents b409c2486353
children a03ff8633507
files filter.xml macros.xml test-data/blobs.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_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 81 files changed, 74 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- a/filter.xml	Wed Sep 22 21:11:51 2021 +0000
+++ b/filter.xml	Wed Nov 08 14:44:39 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="scanpy_filter" name="Filter" 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"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -52,7 +52,6 @@
     groupby='$method.groupby',
     #end if
     use_raw=$method.use_raw,
-    log=$method.log,
     key_added='$method.key_added',
     min_in_group_fraction=$method.min_in_group_fraction,
     max_out_group_fraction=$method.max_out_group_fraction,
@@ -173,7 +172,6 @@
                     <expand macro="sanitize_query" />
                 </param>
                 <expand macro="param_use_raw"/>
-                <expand macro="param_log"/>
                 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values">
                     <expand macro="sanitize_query" />
                 </param>
@@ -228,8 +226,8 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
-            <!-- test 0 -->
+        <test expect_num_outputs="2">
+            <!-- test 1 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.filter_cells"/>
@@ -252,8 +250,8 @@
             </output>
             <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 1 -->
+        <test expect_num_outputs="2">
+            <!-- test 2 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.filter_cells"/>
@@ -274,8 +272,8 @@
             </output>
             <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 2 -->
+        <test expect_num_outputs="2">
+            <!-- test 3 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.filter_genes"/>
@@ -295,36 +293,41 @@
             </output>
             <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <!-- <test> -->
-        <!--     <!-\- test 3 -\-> -->
-        <!--     <!-\- Input dataset appears to be missing rank_genes_groups key... -\-> -->
-        <!--     <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> -->
-        <!--     <conditional name="method"> -->
-        <!--         <param name="method" value="tl.filter_rank_genes_groups"/> -->
-        <!--         <param name="key" value="rank_genes_groups"/> -->
-        <!--         <param name="use_raw" value="False"/> -->
-        <!--         <param name="log" value="False"/> -->
-        <!--         <param name="key_added" value="rank_genes_groups_filtered"/> -->
-        <!--         <param name="min_in_group_fraction" value="0.25"/> -->
-        <!--         <param name="max_out_group_fraction" value="0.5"/> -->
-        <!--         <param name="min_fold_change" value="3"/> -->
-        <!--     </conditional> -->
-        <!--     <output name="hidden_output"> -->
-        <!--         <assert_contents> -->
-        <!--             <has_text_matching expression="tl.filter_rank_genes_groups"/> -->
-        <!--             <has_text_matching expression="key='rank_genes_groups'"/> -->
-        <!--             <has_text_matching expression="use_raw=False"/> -->
-        <!--             <has_text_matching expression="log=False"/> -->
-        <!--             <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> -->
-        <!--             <has_text_matching expression="min_in_group_fraction=0.25"/> -->
-        <!--             <has_text_matching expression="max_out_group_fraction=0.5"/> -->
-        <!--             <has_text_matching expression="min_fold_change=3"/> -->
-        <!--         </assert_contents> -->
-        <!--     </output> -->
-        <!--     <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> -->
-        <!-- </test> -->
-        <test>
-            <!-- test 4 -->
+
+        <!--  test 4 -->
+        <!-- Fails to write to anndata after tl.filter_rank_genes_groups
+             Issue has been reported here: https://github.com/scverse/anndata/issues/726
+             The current fix is: del adata.uns['rank_genes_groups_filtered']  -->
+        <!--<test expect_num_outputs="2">
+            <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
+            <conditional name="method">
+                <param name="method" value="tl.filter_rank_genes_groups"/>
+                <param name="key" value="rank_genes_groups"/>
+                <param name="use_raw" value="False"/>
+                <param name="key_added" value="rank_genes_groups_filtered"/>
+                <param name="min_in_group_fraction" value="0.25"/>
+                <param name="max_out_group_fraction" value="0.5"/>
+                <param name="min_fold_change" value="3"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="tl.filter_rank_genes_groups"/>
+                    <has_text_matching expression="key='rank_genes_groups'"/>
+                    <has_text_matching expression="use_raw=False"/>
+                    <has_text_matching expression="log=False"/>
+                    <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
+                    <has_text_matching expression="min_in_group_fraction=0.25"/>
+                    <has_text_matching expression="max_out_group_fraction=0.5"/>
+                    <has_text_matching expression="min_fold_change=3"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test>-->
+        <test expect_num_outputs="2">
+            <!-- test 5 -->
             <param name="adata" value="blobs.h5ad"/>
             <conditional name="method">
                 <param name="method" value="pp.highly_variable_genes"/>
@@ -353,8 +356,8 @@
             </output>
             <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/>
         </test>
-        <test>
-            <!-- test 5 -->
+        <test expect_num_outputs="2">
+            <!-- test 6 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.highly_variable_genes"/>
@@ -379,8 +382,8 @@
             </output>
             <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/>
         </test>
-        <test>
-            <!-- test 6 -->
+        <test expect_num_outputs="2">
+            <!-- test 7 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.subsample"/>
@@ -402,8 +405,8 @@
             </output>
             <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 7 -->
+        <test expect_num_outputs="2">
+            <!-- test 8 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.subsample"/>
@@ -425,8 +428,8 @@
             </output>
             <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <test>
-            <!-- test 8 -->
+        <test expect_num_outputs="2">
+            <!-- test 9 -->
             <param name="adata" value="random-randint.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.downsample_counts"/>
@@ -461,7 +464,7 @@
 `max_counts`, `max_genes` per call.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_cells.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_cells.html>`__
 
 
 Filter genes based on number of cells or counts (`pp.filter_genes`)
@@ -475,14 +478,14 @@
 `max_counts`, `max_cells` per call.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_genes.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_genes.html>`__
 
 
 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`)
 ==========================================================================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.filter_rank_genes_groups.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__
 
 
 Annotate highly variable genes (`pp.highly_variable_genes`)
@@ -497,7 +500,7 @@
 ======================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.subsample.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.subsample.html>`__
 
 Downsample counts (`pp.downsample_counts`)
 ==========================================
@@ -506,7 +509,7 @@
 has been implemented by M. D. Luecken.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.downsample_counts.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.downsample_counts.html>`__
 
 
     ]]></help>
--- a/macros.xml	Wed Sep 22 21:11:51 2021 +0000
+++ b/macros.xml	Wed Nov 08 14:44:39 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) != ''
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