diff remove_confounders.xml @ 11:73ab2ac53d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d

--- a/remove_confounders.xml	Wed Sep 22 21:10:58 2021 +0000
+++ b/remove_confounders.xml	Wed Nov 08 14:45:35 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="scanpy_remove_confounders" name="Remove confounders" 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"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@
@@ -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://icb-scanpy.readthedocs-hosted.com/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://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.combat.html>`__
 
 
     ]]></help>