add tests and do not copy anndata

Author: pavanvidem

tools/celltypist/celltypist.xml

@@ -10,9 +10,8 @@
         <requirement type="package" version="@TOOL_VERSION@">celltypist</requirement>
     </requirements>
     <command><![CDATA[
-cp '$adata' 'anndata.h5ad' &&
 cat '$script_file' &&
-python '$script_file' &&
+python '$script_file'
     ]]>
     </command>
     <configfiles>
@@ -21,12 +20,17 @@ import scanpy as sc
 import celltypist
 from celltypist import models
 
-adata = sc.read_h5ad('anndata.h5ad') models.download_models(models='$model_name', cache_dir='./celltypist_models_cache')
-model = models.Model.load(models='$model_name', cache_dir='./celltypist_models_cache')
+adata = sc.read_h5ad('$adata')
+models.download_models(model='$model_name')
+model = models.Model.load(model='$model_name')
 predictions = celltypist.annotate(adata,
                 model=model,
-                majority_voting=$majority_voting,
+#if $majority_voting
+                majority_voting=True,
+#end if
+#if $transpose_input
                 transpose_input=$transpose_input,
+#end if
                 mode='$mode',
                 p_thres=$p_thres,
                 min_prop=$min_prop)
@@ -52,24 +56,43 @@ adata.write_h5ad('$anndata_out', compression='gzip')
             <option value="best match">Choose the cell type with the largest score/probability as the final prediction</option>
             <option value="prob match">Enable a multi-label classification utilising a probability threshold</option>
         </param>
-        <param name="p_thres" type="float" label="Probability threshold" value="0.5" />
-        <param name="min_prop" type="float" label="Minimum proportion for cell type assignment" value="0.05" />
-        <param name="reference" type="text" label="Reference column in AnnData.obs for dotplot" value="cell_type" />
-        <param name="prediction" type="text" label="Prediction column in AnnData.obs for dotplot" value="predicted_labels" />
+        <param name="p_thres" type="float" value="0.5" min="0" max="1" label="Probability threshold for the multi-label classification" help="Ignored if mode is best match." />
+        <param name="min_prop" type="float" value="0" min="0" max="1" label="The minimum proportion of cells required to support naming of the subcluster by this cell type" help="Ignored if majority_voting is set to False"/>
     </inputs>
     <outputs>
         <data name="anndata_out" format="h5ad" label="${tool.name} on ${on_string}: AnnData with celltype annotations" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="adata" location="https://celltypist.cog.sanger.ac.uk/Notebook_demo_data/demo_500_cells.h5ad"/>
             <param name="model_name" value="Immune_All_Low.pkl" />
             <param name="majority_voting" value="True" />
-            <param name="transpose_input" value="False" />
             <param name="mode" value="best match" />
             <param name="p_thres" value="0.5" />
             <param name="min_prop" value="0.05" />
-            <output name="anndata_out" file="expected_celltypist_output.h5ad" />
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/predicted_labels"/>
+                    <has_h5_keys keys="obs/over_clustering"/>
+                    <has_h5_keys keys="obs/majority_voting"/>
+                    <has_h5_keys keys="obs/conf_score"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="adata" location="https://celltypist.cog.sanger.ac.uk/Notebook_demo_data/demo_500_cells.h5ad"/>
+            <param name="model_name" value="Immune_All_High.pkl" />
+            <param name="majority_voting" value="False" />
+            <param name="mode" value="prob match" />
+            <param name="p_thres" value="0.5" />
+            <param name="min_prop" value="0.05" />
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/predicted_labels"/>
+                    <has_h5_keys keys="obs/conf_score"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" file="celltypist_annotated.h5ad" />
         </test>
     </tests>
     <help><![CDATA[