--- a/remove_confounders.xml	Wed Sep 22 21:03:44 2021 +0000
+++ b/remove_confounders.xml	Wed Jul 31 18:05:53 2024 +0000
@@ -1,9 +1,9 @@
-<tool id="scanpy_remove_confounders" name="Remove confounders" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_remove_confounders" name="Remove confounders" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description>with scanpy</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@
@@ -30,13 +30,13 @@
     #for i, filepath in enumerate($methods.extra_adata)
     adata_$i,
     #end for
-    #if str($methods.var_subset) != ''
+    #if $methods.var_subset
     #set $var_subset=([x.strip() for x in str($method.var_subset).split(',')])
     var_subset=$var_subset,
     #end if
     batch_key='$method.batch_key',
     index_unique='$method.index_unique'
-    #if str($methods.batch_categories) != ''
+    #if $methods.batch_categories
     #set $batch_categories=([x.strip() for x in str($method.batch_categories).split(',')])
     batch_categories=$batch_categories,
     #end if
@@ -122,7 +122,7 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 0 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
@@ -140,7 +140,7 @@
             </output>
             <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
-        <!--<test>
+        <!--<test expect_num_outputs="2">
             < test 2 >
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
@@ -153,7 +153,7 @@
             </assert_stdout>
             <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>-->
-        <test>
+        <test expect_num_outputs="2">
             <!-- test 1 -->
             <param name="adata" value="blobs.h5ad" />
             <conditional name="method">
@@ -180,7 +180,7 @@
 inspired by Seurat's `regressOut` function in R.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.regress_out.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.regress_out.html>`__
 
 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`
 ==================================================================================
@@ -191,7 +191,7 @@
 Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.api.pp.mnn_correct.html>`__
+<https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.mnn_correct.html>`__
 
 
 Correct batch effects with ComBat function (`pp.combat`)
@@ -200,7 +200,7 @@
 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.combat.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.combat.html>`__
 
 
     ]]></help>