Mercurial > repos > ebi-gxa > scanpy_find_markers

diff scanpy-find-markers.xml @ 29:81c34e67f262 draft

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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 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:28:49 +0000
parents eb01a7e59e9a
children 64259337506f
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--- a/scanpy-find-markers.xml	Thu Oct 28 10:04:02 2021 +0000
+++ b/scanpy-find-markers.xml	Thu Feb 16 13:28:49 2023 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -97,7 +97,6 @@
       <param name="input_obj_file" value="louvain_1.0"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <param name="output_tsv" value="true"/>
       <param name="n_genes" value="50"/>
       <param name="output_markers" value="true"/>
       <param name="default" value="false"/>
@@ -111,8 +110,7 @@
     <test>
       <param name="input_obj_file" value="louvain_1.0"/>
       <param name="input_format" value="anndata"/>
-      <param name="output_format" value="anndata"/>
-      <param name="output_tsv" value="true"/>
+      <param name="output_format" value="no_matrix_output"/>
       <param name="n_genes" value="50"/>
       <param name="output_markers" value="true"/>
       <param name="default" value="false"/>
@@ -120,7 +118,6 @@
       <param name="key_added" value="GROUPBY_marker"/>
       <param name="method" value="t-test_overestim_var"/>
       <param name="rankby_abs" value="false"/>
-      <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
       <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
     </test>
   </tests>