Mercurial > repos > ebi-gxa > scanpy_integrate_harmony

diff scanpy-integrate-harmony.xml @ 14:c354af93f567 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:15 +0000
parents 18e01a7c55c6
children
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--- a/scanpy-integrate-harmony.xml	Fri Oct 13 14:08:00 2023 +0000
+++ b/scanpy-integrate-harmony.xml	Tue Feb 27 16:43:15 2024 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
+<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>adjust principal components for variables that might introduce batch effect</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -8,7 +8,7 @@
   <command detect_errors="exit_code"><![CDATA[
 #if $batch_key
   ln -s '${input_obj_file}' input.h5 &&
-  PYTHONIOENCODING=utf-8 scanpy-integrate harmony
+  PYTHONIOENCODING=utf-8 scanpy-cli integrate harmony
   --batch-key '${batch_key}'
   #if $basis
     --basis '${basis}'
@@ -114,13 +114,17 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="batch_key" value="louvain"/>
-      <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" ftype="h5">
+        <assert_contents>
+          <has_h5_keys keys="obsm/X_pca_harmony"/>
+        </assert_contents>
+      </output>
     </test>
     <test>
       <param name="input_obj_file" value="find_cluster.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
     </test>
   </tests>