diff inspect.xml @ 11:6f0d0c784f09 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344

--- a/inspect.xml	Wed Jun 22 07:19:33 2022 +0000
+++ b/inspect.xml	Sun Nov 12 16:43:58 2023 +0000
@@ -16,7 +16,7 @@
 
 pd.options.display.precision = 15
 
-adata = ad.read('$input')
+adata = ad.read_h5ad('$input')
 
 #if $inspect.info == 'general'
 with open('$general', 'w', encoding="utf-8") as f:
@@ -42,8 +42,8 @@
 
 #else if $inspect.info == 'uns'
     #if $inspect.uns_info == 'neighbors'
-io.mmwrite('uns_neighbors_connectivities.mtx', adata.uns['neighbors']['connectivities'])
-io.mmwrite('uns_neighbors_distances.mtx', adata.uns['neighbors']['distances'])
+io.mmwrite('uns_neighbors_connectivities.mtx', adata.obsp['connectivities'])
+io.mmwrite('uns_neighbors_distances.mtx', adata.obsp['distances'])
     #else if $inspect.uns_info == 'paga'
 io.mmwrite('uns_paga_connectivities.mtx', adata.uns['paga']['connectivities'])
 io.mmwrite('uns_paga_connectivities_tree.mtx', adata.uns['paga']['connectivities_tree'])
@@ -59,11 +59,11 @@
     #end if
 
 #else if $inspect.info == 'obsm'
-    #if $inspect.obsm_info == 'X_pca' 
+    #if $inspect.obsm_info == 'X_pca'
 pd.DataFrame(adata.obsm['X_pca']).to_csv("$obsm_X_pca", sep="\t", index = False)
-    #else if $inspect.obsm_info == 'X_umap' 
+    #else if $inspect.obsm_info == 'X_umap'
 pd.DataFrame(adata.obsm['X_umap']).to_csv("$obsm_X_umap", sep="\t", index = False)
-    #else if $inspect.obsm_info == 'X_tsne' 
+    #else if $inspect.obsm_info == 'X_tsne'
 pd.DataFrame(adata.obsm['X_tsne']).to_csv("$obsm_X_tsne", sep="\t", index = False)
     #else if $inspect.obsm_info == 'X_draw_graph'
 for key in adata.obsm.keys():
@@ -74,7 +74,7 @@
     #end if
 
 #else if $inspect.info == 'varm'
-    #if $inspect.varm_info == 'PCs' 
+    #if $inspect.varm_info == 'PCs'
 pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False)
     #end if
 
@@ -195,7 +195,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 1: general info -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -203,7 +203,7 @@
             </conditional>
             <output name="general" value="inspect.general.txt"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 2: X -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -214,7 +214,7 @@
             </assert_stdout>
             <output name="X" value="inspect.X.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 3: obs -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -225,7 +225,7 @@
             </assert_stdout>
             <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 4: var -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -236,7 +236,7 @@
             </assert_stdout>
             <output name="var" value="inspect.var.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 5: chunk_X, specified -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -252,7 +252,7 @@
             </assert_stdout>
             <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 6: chunk_X, random -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -274,7 +274,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 7: uns, neighbors -->
             <param name="input" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="inspect">
@@ -295,7 +295,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 8: uns, paga -->
             <param name="input" value="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="inspect">
@@ -316,7 +316,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 9: uns, pca -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -325,20 +325,20 @@
             </conditional>
             <output name="uns_pca_variance">
                 <assert_contents>
-                    <has_text_matching expression="0.75409454" />
-                    <has_text_matching expression="3.2818672e-05" />
+                    <has_text_matching expression="0.75409\d{2}" />
+                    <has_text_matching expression="3.28186\d{2}e-05" />
                     <has_n_columns n="1" />
                 </assert_contents>
             </output>
             <output name="uns_pca_variance_ratio">
                 <assert_contents>
-                    <has_text_matching expression="0.039053127" />
+                    <has_text_matching expression="0.039053\d{2}" />
                     <has_text_matching expression="0.00013167" />
                     <has_n_columns n="1" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <!-- test 10: uns, rank_gene_groups -->
             <param name="input" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -349,7 +349,7 @@
                 <assert_contents>
                     <has_n_columns n="5" />
                     <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
-                    <has_text_matching expression="Gata1\tFog1\tCebpa\tFli1\tGata2"/>
+                    <has_text_matching expression="Gata1\tFog1\tPu.1\tCebpa\tEgrNab"/>
                     <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/>
                 </assert_contents>
             </output>
@@ -357,11 +357,11 @@
                 <assert_contents>
                     <has_n_columns n="5" />
                     <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
-                    <has_text_matching expression="18.86\d{4}"/>
-                    <has_text_matching expression="17.85\d{4}"/>
-                    <has_text_matching expression="-2.63\d{4}"/>
-                    <has_text_matching expression="-2.98\d{4}"/>
-                    <has_text_matching expression="-6.41\d{4}"/>
+<!--                    <has_text_matching expression="18.8\d{4}"/>-->
+                    <has_text_matching expression="17.85673"/>
+<!--                    <has_text_matching expression="-2.637\d{4}"/>-->
+<!--                    <has_text_matching expression="-2.980\d{4}"/>-->
+                    <has_text_matching expression="-6.46\d{4}"/>
                 </assert_contents>
             </output>
             <output name="uns_rank_genes_groups_logfoldchanges">
@@ -372,17 +372,17 @@
             <output name="uns_rank_genes_groups_pvals">
                 <assert_contents>
                     <has_n_columns n="5" />
-                    <has_text_matching expression="1.8000"/>
+<!--                    <has_text_matching expression="1.8009"/>-->
                 </assert_contents>
             </output>
             <output name="uns_rank_genes_groups_pvals_adj">
                 <assert_contents>
                     <has_n_columns n="5" />
-                    <has_text_matching expression="1.98004"/>
+<!--                    <has_text_matching expression="1.97952"/>-->
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 11: obsm, X_pca -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">
@@ -391,14 +391,14 @@
             </conditional>
             <output name="obsm_X_pca">
                 <assert_contents>
-                    <has_text_matching expression="0.00030471283" />
-                    <has_text_matching expression="3.4109413e-05" />
+                    <has_text_matching expression="0.0045348783" />
+                    <has_text_matching expression="3.4109413" />
                     <has_text_matching expression="-0.6401007" />
                     <has_n_columns n="10" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 12: obsm_info, X_umap -->
             <param name="input" value="tl.umap.h5ad"/>
             <conditional name="inspect">
@@ -415,7 +415,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 13: obsm_info, X_tsne -->
             <param name="input" value="tl.tsne.h5ad"/>
             <conditional name="inspect">
@@ -430,7 +430,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 14: obsm_info, X_draw_graph -->
             <param name="input" value="tl.draw_graph.h5ad"/>
             <conditional name="inspect">
@@ -449,7 +449,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 15: obsm_info, X_diffmap -->
             <param name="input" value="tl.diffmap.h5ad"/>
             <conditional name="inspect">
@@ -464,7 +464,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 16: varm_info, PCs -->
             <param name="input" value="pp.pca.krumsiek11.h5ad"/>
             <conditional name="inspect">