--- a/manipulate.xml	Wed Jun 22 07:21:03 2022 +0000
+++ b/manipulate.xml	Sun Nov 12 16:42:25 2023 +0000
@@ -20,11 +20,11 @@
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
 
-adata = ad.read('$input')
+adata = ad.read_h5ad('$input')
 
 #if $manipulate.function == 'concatenate'
     #for i, filepath in enumerate($manipulate.other_adatas)
-adata_$i = ad.read('$filepath')
+adata_$i = ad.read_h5ad('$filepath')
     #end for
 adata = adata.concatenate(
     #for i, filepath in enumerate($manipulate.other_adatas)
@@ -174,7 +174,7 @@
                     <option value="var">Variables (var)</option>
                     <option value="obs">Observations (obs)</option>
                 </param>
-                <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 
+                <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
                     help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
             </when>
             <when value="filter">
@@ -289,12 +289,12 @@
             <conditional name="manipulate">
                 <param name="function" value="rename_categories"/>
                 <param name="key" value="cell_type"/>
-                <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
+                <param name="categories" value="Ery, Mk, Mo, progenitor"/>
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.rename_categories"/>
                 <has_text_matching expression="key='cell_type'"/>
-                <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
+                <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/>
             </assert_stdout>
             <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>